...I think the solution to your proposed problem of disc golfers holing out and starting a new hole within one ball golf hole is to push both the target and the tee off the fairway. By doing so, the disc golfers can putt out and go to the next tee and then wait for the ball golfers to tee off from a safe, out of the way location in which they can watch for incoming balls if necessary.
Have you seen ball golfers play? There is no safe, out of the way location. The only safe way to play in front of golfers is if they don't hit, or you are on the next hole. To keep them from hitting, you need to be visible.
The speed at which disc golfers putt is unbelievable to a golfer. To golfers, disc golfers clear the hole in the blink of an eye. The golfers learn that the disc golfers will all putt, go to the next tee, throw and walk out of range in the time it can take a regular golfer to miss his first of 3 putts.
The speed at which disc golfers play two holes has a lot of overlap with the speed at which golfers play one. So, golfers getting stuck behind another group of golfers is just about as likely as golfers getting stuck behind disc golfers, or disc golfers getting stuck behind golfers, or disc golfer getting stuck behind disc golfers.
The same etiquette exists for these situations for both golfers and disc golfers, so they know what to do.
Again, though, it varies by the type of golfer.
At Fort Snelling, an executive 9-hiole with some real golf challenges, there are more serious (and skilled) golfers. There, the best move is to let the golfers tee off first. They hit the ball beyond the disc golf target, so the disc golfers can then play unfettered. Usually, the two groups won't see each other after that, except maybe the disc golfers would politely wait for the golfers to putt on the first hole before throwing at the second disc golf hole - so the golfers aren't distracted by something flying in their peripheral vision.
At Wirth Par 3, the golf course is the easiest golf course around, so all the players are unskilled. Think 7-year olds out with their grandmothers. There, the golfers let the disc golfers go first because they would be embarrassed to have someone watch them swing, and because the disc golfers will get out of the way quickly.
All that being said, don't add disc golf unless the course is so empty that it is desperate, or you can separate the course entirely (either in space or time) from the golfers.