Can I apply water-based polyurethane over an oil based stain?
Short answer: yes.
Longer answer: if you wait for the oil-based stain to properly 'dry' (cure) it's no longer oily. This is because the curing process for oil is polymerisation, and polymerised oil is akin to resin.
So far so good, but am I likely to have problems with poly adhesion in the future because I mismatched the base types of the stain and poly?
Obviously the time between stain and varnish application will be a factor. But if you didn't experience major problems with beading of the waterbased poly as you were applying it I think you're OK.
If you want to take an extra precaution you can use shellac as an intermediate coat. This can also be used to speed up the process because the shellac can go directly onto oiled wood without waiting for the oil to dry. Then you can overcoat the shellac with your final finish after just waiting for the shellac to dry enough, perhaps as little as an hour.
Even with "super-blonde" shellac there's some yellow colour of course, but it's applied very thinly so the effect should be minimal.