My concern isn't so much how it looks in my editor, but everywhere else. I doubt the internets are going to change their fonts just for us. Hopefully Perlmonks would, because that's where I was looking when trying to distinguish.
In fact, look at this: ~ <---- without code markup
and this: ~ <---- with code markup
Without increasing my font size, I can just barely tell that the tilde is a tilde without the code markup. With the code markup, it is hopeless.
In the event that it is easily distinguishable for you, here is a screenshot of this entry on OS X; Chrome; View:Actual Size.