I agree with the general opinion that it's probably better to wait. But if you were to apply, my opinion is that you should get through just fine for the following facts:
(a) Though they can review entire history, the normal procedure is not to question their own prior decisions. Unless there's a glaring problem, like fraud, it'd be unlikely they'd go back to reverse prior approvals.
(b) You had genuine employment on which LC and 140 was approved. (Be sure to save paystubs etc to show this). You continued to work until they terminated you (effectively the date the last paycheck was issued).
(c) After 5 years as a permanent resident, USCIS can't just administratively revoke your GC. They need to go to an immigration judge etc, and as far as I can see from history here and elsewhere, they do this only when they have a strong motive, such as someone with a criminal incident, etc. No fraud, no criminal background, >5 years as permanent resident -- dude.. you should worry more about swine flu or something.
(d) Your wife's case is even harder to deny if she applies alone. Because N400 is her application alone, they are reviewing her file, not yours. To initiate a review on your file, they need to establish a reason to suspect validity of her GC. There is no such reason. And even if there is, because it's >5 years, they'll need to meet a much higher bar of proof to revoke your GC, such as showing there was fraud. It's a legally harder standard to meet and I doubt that exists in your case.
(e) The only "problem" I see is actually your employer's headache - if you were on a H1B and they didn't terminate you [you didn't sign a termination notice and there's no conclusive proof of one being delivered to you] -- they could be forced to pay back wages you up until you took up a new job. In which case, you were always employed. I don't expect this to happen, but we're discussing a theoretical legal problem, and the theoretical solution is in your favor.
Bottom line is, your GC is in good grounds and your N400 will come through (perhaps with a few extra months of "administrative reviews" -- read nervous waiting time for you): So it's up to you and in the end, how much patience you have with paperwork and USCIS! My opinion.