We were doing Emalon, so not anything important, and we hadn't started so no one was saved. In this situation, is it understood by everyone that a guildy comes first? Or would it be considered bad form to kick out a pug even if they hadn't been saved? I know I don't like it when I am treated that way, but I may be over-sensitive. I know I would consider kicking out a pug for a guildy after the pug had been saved would be unacceptable, unless they were just fail.
So yeah, what is the general consensus on what is fair and expected?
I'm sure our readers will have plenty to say on this topic in the comments, but here is my take on it.
PUG players are not, in fact, disposable. Looking at them in this way is a disservice to your own guild. Many people write me asking how to recruit players. Running raids with PUGs is a great way to meet players who are searching for a guild. If you boot them the second your own guild members decide to show up, even at the start of a raid, you're making a bad impression. If you make a habit of booting PUG players, that impression could cost you recruits in the long run.
That doesn't mean you can't. By all means, do it if you think it will keep your own members happy. They're the people you need to look after, when you get right down to it. However, if your members are late to the raid, do they really deserve a slot? By inviting them, you might be improving your raid's chance of success. But you're also sending the message that it's OK to be late. You say it's not the issue, but I bring it up anyway for others to consider in their own circumstances.
For your scenario, it's an Emalon run, so it's probably not something you scheduled. That makes the situation a little less clear-cut. The best thing to do in my opinion is to ask if anyone would mind leaving the raid to make room for some people from your guild. Most likely, no one will volunteer, but you might be surprised. If someone does, put them on your friend's list. He or she is a person worth knowing, and someday you might be able to return the favor. If no one does, and you run with them anyway, that leaves a good impression of your guild. Now they know you were willing to run with them even though you could have replaced them.
If you've decided you're going to replace people with your own, I'd only take this step while the raid is still getting itself organized. When you've already started pulling, swapping people is just going to bog down the entire process. People might get impatient and leave. Then you'll go from a surplus of raiders to a deficit, and you'll have to waste even more time.
Still, the bottom line in this case is that it's just Emalon. Unless Jubei'Thos is the worst server in WoW, your guild members can go PUG it with another group.
If replacing people is what you want to do as a matter of policy, then tell your PUGs that up front. Inform them that their slot is contingent on no other guild members being available. They could still complain about it, but at least you warned them.
Obviously, as you state, booting someone who is saved to your instance is a pretty terrible thing to do. I'd only take this step if a PUG player was wiping us or disrupting the raid somehow.
Now, this is all my opinion and advice. Alarm is asking for the etiquette. Most guilds in my experience wouldn't even blink. They'd drop those PUG players like a sack of potatoes and slot up their own members before you could even ask for the Vent info. And I'd have to say that most people would expect it. After all, PUG players are notorious for abandoning runs with no warning. Why should guilds show any consideration toward them?
It's a cold world out there. But we as officers and raid leaders don't have to act that way. Our behavior serves as an example to others. We set the tone for our server. All of our decisions add up over the long run and they determine what is acceptable. Ultimately, we make our own etiquette. So, Alarm, my question to you is, what do you want the etiquette to be?