OK, I sometimes run into dungeons with no altars of my alignment, and the altars I find have priests who I'm going to have to kill to convert them.
I've never done that deliberately, but did once due to a typo...., so I know what happens.
Is it pretty much expected that we murder priests in this situation?
If you have reflection, than yeah, it's sometimes not a bad idea.
Get a nice pet, such as a vampire lord, and let the pet do the killing. You avoid the consequences of murder if non-chaotic, and there is much less risk because priests don't cast spells at pets.
You may even want to do this (once you have donated to the priest) if you don't need to do this to get an altar. You can get your money back to donate to another priest, and the priest usually has a robe and several spellbooks which are useful if you are a spellcaster.
I had a pet dragon once, that I'd got from stepping on a poly trap while wearing sdsm, and then laying an egg and hatching it... it killed and ate the aligned priest on minetown when I went back there to donate... So pets can be an effective way to dispose of an unwanted priest...