Recent gnome-terminal handles these much more safely. If you paste in a newline, whether from primary or clipboard, the terminal puts a newline into your command, but doesn't press enter for you.
I'm having difficulty imagining this. I know of some who warn on multiline paste, but how exactly is it possible to "put a newline" but not "press enter"? Just emit a newline as output without sending as input?
There's lots of other programs that use C-q for quoting, for example emacs, and readline probably copied it from there in the first place.
When pasting text, it's a different code path than quoting. The terminal surely knows when text is being pasted. If nothing else, a simple heuristic based on typing speed is enough to tell apart typing and pasting.