Congratulations! It's been a while since I was pregnant, but I traveled quite a bit when I was and was quite comfortable even on 11-hour flights. As long as the pregnancy is progressing smoothly, I wouldn't expect your wife to be uncomfortable that early on in her pregnancy. She may want to get a seat close to the lav though as she gets bigger. Traveling in business would surely be nice for her though so she can use the foot rests (of course, that's true pregnant or not ).

I seem to recall a thread on this forum a while back about traveling during the last stage of pregnancy. You may want to look for that for some tips too.