I just got 2 pairs of trousers back from the tailors yesterday actually. Same issue as you - just wanted them tapered / slimmed down as they were too billowing for my legs. They look good, though I actually wish I had been a bit braver and gone slimmer again.
Never done it with jeans though. Unless it's some strange "twisted" fit or something, I don't see there being a problem.
Best thing to do though is to find a brand of slim jeans (rather than skinny) which you are happy with. I started a thread on here a couple of months ago on just that issue and got some good advice. Have a search.