"Auto Flush Notes 2" by Dennis DeSantis is one of those Max for Live devices that once you see what it does, you can't believe how you could go without it. At least, I had wanted these functions for a long time. It automatically stops all notes once the transport is stopped.
Add it to any MIDI track you wish to use it on, quickly configure it. Done.
This way for heaps more Max for Live devices & tips.