Although I don't have a lot of historical info to go on, at least later muzzle loaders always used a patch around the "bullet" when it was rammed down onto the powder charge. Where rapid loading might be needed, the fit might not have been particularly tight, but the patch was nearly always greased (or waxed) and would be expected to quite effectively seal the bullet in the barrel so that pouring water down the barrel would be unlikely, at least over a short time, to get sufficient water to the main powder charge to cause much harm to the powder. If left long enough to have a reliable effect moving the gun in almost any way would be likely to reveal the deed by water, not absorbed into the powder, running back out of the barrel.

The primer, or "flash charge" in the pan (often called the "flash pan" in fact) where the flint (or other device) ignited it would be easily rendered inert by even a small amount of water.

The flame produced by the flash charge reached the main powder charge through an open "flash hole" that would possibly admit some water to the main charge if a fairly large amount of water was applied there. The flash hole, however, was generally quite small and it might not have been large enough to avoid a "miniscus" block, making it difficult to destroy the main charge without more than casual pressure or by "squirting" water at the hole with some force/velocity. Getting enough water through the flash hole to completely destroy the main charge would be a bit like trying to put toothpaste back into the tube.

Although a well-knapped flint can produce a significant visible bunch of sparks, the sparks are generally small, and carry little heat. It's a tossup whether it would be necessary to "deactivate" even the entire flash pan charge, or whether a small spit sufficient to quench the sparks on a "dampish" surface of the powder in the pan would suffice to prevent ignition of the charge and would render the gun useless without being obvious except under very close inspection.

In rare but fairly recent usage, I've heard she "spit in his pan" used with the meaning of "she rejected (forcefully) his planned activity," in a group not having a particular knowledge of black power so far as I know - although I'll admit it was a rather strange group. (She, of course, being invariably a spouse?) I suspect this is a surviving form of what was originally intended in the lyric(?) - or maybe not(?).

John