The fundamental misunderstandings here are related to two concepts:
- Conservation (atoms are conserved, molecules are not)
- A mole is just a number (like the chemist's dozen)
I would start with conservation, then move on to moles.
Explaining why atoms are conserved, but not moles
For second-graders, hands-on activities are probably best, so molecular models or something similar would be a good approach. I like your example using two molecules - if you can get some models, you could try having groups of students start with two (or more - 4+ would make it easier to see) molecules of $\ce{SO3}$. Have them count the number of molecules and the number of each atom. Write the results down where everyone can see them. Then, have them do the "reaction" - let them take apart the molecules and put them back together to make$\ce{O2}$ and $\ce{SO2}$. Again, have them count the molecules and the atoms. Show them that the number of atoms stays the same (for each element and in total), but the number of molecules can change.
Once your students are comfortable with this idea, introduce the concept of moles as a way of counting very large numbers. This is the more difficult part, and in my experience is the "make or break" concept for most chemistry students.
A mole is just a very large number
Goal: The number of atoms in macroscopic samples is huge
You can motivate the discussion by calculating the number of molecules/atoms in very small samples. In my classes (college level) I use the number of molecules in one mL of hydrogen gas at STP, and show that if you counted one molecule per second, it would take longer than the age of the universe (a lot longer) to count them all. Sometimes I use the number of silicon atoms in a bag of sand and show them that it is larger (much larger) than the number of stars in the universe. Other examples would work as well - the idea is to get them thinking about the largest quantity that they can possibly imagine and show them that the number of atoms in even a small amount of matter is much larger than that.
Goal: A mole is just a number
Now you want to link this to moles. I start with the concept of a dozen. I ask things like "how many donuts are in a dozen?" "Ok, how many cookies?" "How many cats?" "How many people" until someone points out that it's always 12. Then I ask them why we say a dozen instead of 12. If they don't figure it out quickly on their own, I tell them that for bakers and their customers, it is a convenient way to count stuff. Then I tell them chemists also have a convenient way to count atoms and molecules, which is good because there are a lot of them! The number they use is called a mole, and similarly to how a dozen = 12 of anything, a mole = 6.022 x 10^23 of anything.
Goal: A mole is a HUGE number
Depending on how good the students are with scientific notation, you might want to actually write out that number of zeroes - it's an impressive demonstration! When there is time, I also like to demonstrate the scale by comparing it to different things as the number of zeroes grows. For example, I say (or have them say) "thousand," "million," "billion," "trillion," for every three zeroes. At around 11 zeroes I start comparing it to unimaginably large things. As examples:
- The number of stars in the Milky Way galaxy is about 100 billion ($1 \times 10^{11}$).
- The number of sheets of paper that would fit in a stack between Earth and the moon is about 4 trillion ($4 \times 10^{12}$).
- The number that would fit between Earth and Mars (at their average distance) is about $2 \times 10^{15}$.
- Age of the universe in seconds is $4 \times 10^{17}$.
- There are $10^{22}$ stars in the universe.
I think that this is effective because it connects the concept of moles being huge and the number of atoms being huge to a bunch of astonishing facts - people tend to remember weird little surprising facts, and because of the way memories form, the moles stuff gets stored along with it, leading to an artificially created "intuitive" understanding of the size scale of moles and their relationship to counting atoms.
Now you need to tie it all together.
Goal: Moles are used to count atoms and molecules
I connect the concept of a mole being a very large "convenience" number used for counting to the stoichiometry and conservation concepts with a simple exercise. I write out a chemical equation, which in your case would be:
$$
\ce{2SO3 <=> 2SO2 + O2}
$$
Underneath, I write the number of molecules of each, starting with the smallest. So, I would write...
$$
\begin{array}{|c|c|c|c|c|}\hline
\ce{2SO3} & \ce{<=>} & \ce{2SO2} & \ce{O2} \\ \hline
2 \space \rm{molecules} & & 2 \space \rm{molecules} & 1 \space \rm{molecules} \\ \hline
\end{array}
$$
... and say "If we have two molecules of $\ce{SO3}$, we will end up with two molecules of $\ce{SO2}$ and one of $\ce{O2}$." Then I ask them: "What if I start with 10 molecules $\ce{SO3}$?" and let them figure it out, writing on the board as I go. Next, I ask
- "What if I start with 12?"
- "What about a dozen?"
- "How about 100?"
- "A billion?"
- "$6.022 \times 10^{23}$?"
- "A mole?" - at this point, most of them will have the idea
- "10 moles?"
At the end, the board looks like this:
$$
\begin{array}{|c|c|c|c|c|}\hline
\ce{2SO3} & \ce{<=>} & \ce{2SO2} & \ce{O2} \\ \hline
2 \space \rm{molecules} & & 2 \space \rm{molecules} & 1 \space \rm{molecules} \\ \hline
10\space \rm{molecules} & & 10\space \rm{molecules} & 5 \space \rm{molecules} \\ \hline
12\space \rm{molecules} & & 12\space \rm{molecules} & 6 \space \rm{molecules} \\ \hline
1\space \rm{dozen} & & 1\space \rm{dozen} & 0.5 \space \rm{dozen} \\ \hline
100 \space \rm{molecules} & & 100 \space \rm{molecules} & 50 \space \rm{molecules} \\ \hline
1 \times 10^9 \space \rm{molecules} & & 1 \times 10^9\space \rm{molecules} & 0.5 \times 10^9 \space \rm{molecules} \\ \hline
6.022 \times 10^{23} \space \rm{molecules} & & 6.022 \times 10^{23}\space \rm{molecules} & 3.011 \times 10^{23} \space \rm{molecules} \\ \hline
1 \space \rm{mole} & & 1 \space \rm{mole} & 0.5 \space \rm{mole} \\ \hline
10 \space \rm{mole} & & 10 \space \rm{mole} & 5 \space \rm{mole} \\ \hline
\end{array}
$$
At this point most everyone will "get it" - and the advantage of this method is that they sort of figure it out for themselves along the way, which means they will remember it more clearly. If anyone still struggles with the conservation part, you can have them calculate the number of each atom and each molecule for all or some of the examples above, in the same manner as at the beginning of the lesson.