It seems to me that Juliet would do anything to leave the island - even if this means capturing the baby Aaron or killing Claire. It's also quite clear that Charlie would do anything to save both of them.

What if this conflict between Juliet and Charlie's objetives turns out into a tragedy by the end of the season, with Desmond (stopped by Jack) failing to save Charlie from Juliet's determination?

Am I going too far?

Very good point! I can see this happening. If Juliet does anything that looks like it could be endangering Claire, Charlie will be all over her. If Charlie gets in Juliet's way, I wouldn't put it past her to kill him if he is going to mess up her chance to get off the island.
Desmond has his work cut out for him now.

That would be an intesting way for these two plot points to collide.