Go with it!

I've always come upon my best, and most original, ideas that way. If you try to constrain your writing too much, the story may come out feeling constrained, as well.

Also, if you see a "flaw" in your premise now, then it's likely to haunt the entire story anyway (and may evolve into an even bigger issue than you initially thought), better to nip that in the bud now before you put too much work in.

Hope that helps!