In universe - Because the risk was too high.
The only time when the battery life on the Iron Man armour becomes an issue during the battle of New York is when JARVIS alerts Tony that they don't have enough power to get back through the portal once they have sent the nuclear missile through it.
At this stage, Tony Stark can do one of several things;
- Allow the nuclear missile to destroy New York, saving his own life.
- Ask Thor to hit him with lightning, putting the suit under untested conditions and potentially causing the missile to detonate prematurely. It's worth mentioning that at this point in the film, Tony is using a new Iron Man suit to the one he was wearing in the forest, which might handle the lightning in a different way.
- Take the risk involved in making sure that the nuclear missile ends up in a safe place, i.e. the portal.
Although the final option puts Tony in the most danger, it is also the only one that guarantees the nuclear missile will not destroy New York. As such, it is the option that Tony Stark takes, saving the lives of millions of people and ending the battle in one fell swoop.
Out of universe - For character development.
Earlier on in The Avengers/Avengers Assemble, a heated arguement between Steve Rogers and Tony Stark occurs, with Steve saying;
I've seen the footage. The only thing you really fight for is yourself. You're not the guy to make the sacrifice play, to lay down on a wire and let the other guy crawl over you.
To which Tony responds;
I think I would just cut the wire.
This is a clear example of Tony's style of thinking - that there is always another way out, a way for everyone to win.
Naturally, he later finds himself in a situation where he cannot just "cut the wire", and instead has to make the sacrifice play - in this instance, putting himself in harms way by flying the nuclear missile into the portal.