We use (mostly my) add a balls in the Detroit Pinball League with some regularity. You can come up with all kinds of scenarios why this won't work, but it has always been fine. The endless games we have had over the years have, without exception, been DMD games.
As far as scoring goes, we use a first, second, third, fourth place system, so you are playing against 3 other people on the same machine for a given round and score v them. For single player games, you simply write down your score at the end of your game.
Disabling AAB would be game dependent. Plus, it would really hose up the rule set. This was why we (DPL) moved away from plunging extra balls to playing them on EMs and early SS machines. That said, you could study the schematic and come up with something in short order. If you have a WOW variety, you could just unsolder the coil to stop up the WOW. 5 seconds of looking at a Subway schematic shows that unsoldering the "K" (add-a-ball) relay would do the same thing on this machine.