I use jQuery 70% Dojo 30% in my applications and I haven't met any conflicts yet. So I assume they are almost compatible with each other. So you really like jQuery (and there are so many reasons), go head and use it when you can.
The point is Esri API is on top of Dojo and Dojo has its own advantages.So learning more about dojo will only benefit your work. The best case is you get the best from both.