Of course. But when someone is looking for a pug in trade, advertising a guild run doesn't mean that the pug has no chance at loot. Rather, it emphasizes that its probably going to be a little more coordinated and cohesive of a group than just 10 random pugs who happened to get together. The overall expectation of joining a raid as a pug, whether its a guild run or not, is that loot is open to all. If someone is specifically looking for a pug or two to fill up a guild raid and has no intention of letting that person roll on gear, then they should be up front about that. If they are not then they are purposefully being a dick about it.
I am fully aware of Blizzard's policy on scamming and loot. If the pug player does not ask the RL to say what the loot rules are then it is up to the ML to give out that loot however they want. But that doesn't change the fact that the normal expectation upon joining a raid that doesn't state otherwise is that everyone is rolling on gear. A RL that doesn't mention that is not the case when they know that is exactly how they will be doing it is being intentionally deceptive and while not violating Blizzards policies, its still a jackass move.
Also, I don't think that your idea that a pug joining a guild run so that they can get their achievement is something that happens a lot. I've never seen a guild run raid that needed another person or two that wasn't looking for people who already had that achievement or a certain level of gear. I'm sure that it happens, but its not the norm.