I'm hoping there will be a patch in the near future that waters down the spawning a bit.
At least that isn't game ending. I've had some of the best fights from checkpoint attacks. But really I don't find them an issue. Most of the time I can just drive straight through, run over 1 or two enemies, and then outrun any cars that follow. But I've been using the boats and buses A LOT more to mix up the traveling, and even running (whatever route is fastest), so really the ambushes don't bother me much at all.
start growing weary of sneaking by/destroying the same checkpoints over and over again.
See unless you want to take them out every time, why would you? You can drive right through and outrun them, often with just 1 vehicle (2 enemies) following...easy to take out and only interrupts your travel for a few seconds.