In Safari or the app?
The FaceBook app only pester's me when I accidentally tap on the messaging icon. I've got Chat turned off, both on my iPad and in the website, so that might be a factor as well.
I almost never use FaceBook in Safari on the iPad, but that's the only way I know of to send or receive messages on your iPad without the FaceBook Messages app. FaceBook has disable Messages in all their apps. They want it to be a separate app, and aren't inclined to give people the option of not changing their habits.