Clarification
The OP's question seems to indicate that the ground troops are dropped after the air forces are already under attack. This is not so. The land forces are dropped prior to any confrontation, and in fact, they enter combat before any counter air assault by the Na'vi occurs.
Possibly "Plan B"
While "Plan A" was to drop the explosives to level the sacred tree by the air assault, there were unknown factors. They were going into a region that scanners and instrumentation did not function well, while flying a large shuttle through an aerial obstacle course to get to their prime target (recall the comment about loosing some "paint" by the shuttle pilots as they enter into the floating mountains). The lack of instrumentation for targeting may be why they chose to "drop" explosives rather than just missile it to death like Home Tree. This is another oddity about the strategy; why not just fly all the aircraft close and rain missiles down like the Home Tree attack? (I do not have a good answer.) Nevertheless, that was the primary strategy.
However, given the speculative aspect of being able to navigate the larger shuttle in through the mountains and succeed with the drop of explosives, likely the ground forces were a "Plan B." If the shuttle could not make the drop, then Plan B was probably to close in on the tree and take it out at ground level; recall, it was magnitudes of size smaller than the Home Tree.