I don't think that you actually need to be in the US to apply for naturalization. You must be "physically present" which has it's own weird definition and have "continuous residence".
However, logistically, it wouldn't make any sense. Sometime in the first month an a half after your wife applies, the USCIS will want to have her come in and take her fingerprints. Then sometime (between 2 and 8 months later) she'll have to show up for the interview.
Why tempt fate? Wait the 4 or 5 months (it's really good if she isn't out of the country for 6 months or more -- see the guide to naturalization and many of the threads here for why), and then apply. Get the form all filled out and then mail it just as she arrives back in the US.
And, of course, I'm not a lawyer...
