Two ways to deal with that. One is to go through and edit out the snare hits (or possibly use a gate, if you can get it to play nice.) The other is to insert a compressor on the kick, and use the snare direct mic as the key to the sidechain input. Then, every time the snare is hit, the kick signal gets ducked. This is a great way to take the snare out of beater mics, too, I do it all the time!