Personally, I would continue to mix them to make the transition easier. It is unlikely the fact you are mixing the two is causing the GI upset. If he has taken Gentlease since he was 3 mo, and has always been fine with it, why would is be causing problems now? It's not like mixing the milk with it causes any sort of chemical reaction or change in the properties of the formula.
The culprit is likely the lactose in the cow's milk and if lactaid is an easy fix, see how it goes for a few days (which you have probably already done since I am writing this a few days after your post). Having said that, soy milk is so readily available now, I am not sure why it would be a bid deal for you to just jump to that instead.
BTW, my 9 mo has also been on Gentlease nearly all her life and I am also wondering if that will cause problems when I transition her to cow's milk. I asked my Pedi did she think there might be problems since my LO has been taking a formula with much less lactose that standard ones, and she said "probably not". I am curious to see what happens when the time comes....