With a rounded window it really would mess up the saucer just because of all the extra geo it takes to make a square into a circle,
Perhaps I'm just spoiled by Lightwave, but it really shouldn't create such a mess nor should you have to turn a square into a circle - you simply cut a circle-shape into the geometry.
Judging by what you've accomplished with this model already this shouldn't be above your skills.
Yeah it's definitely doable in Maya, and I can definitely do it now.
It's just a question of time, If I were to fix the windows. I would have to do more then trace a circle or a very rounded square, In Maya the Interactive Split Tool is really finicky, there are also curves. There are tons of methods in Maya, it's just time.
Btw just looked up Lightwave, looks interesting. I may have to try it.