You can try uninstalling or if it won't allow that disabling the other gallery. However, the photos aren't stored in that gallery. That is just an app for viewing them. They are stored on the phone.
When you sync the phone to your google account, it doesn't mean it removes them off the phone. It just makes copies of them to the account. Now if you are choosing to delete them from the phone after the copies are made (or they are uploaded) that is different. It may well be that the images are not still in the gallery but it is holding residual info. If that is the case, restarting the phone (turning it off and back on) should clear that up.