How to ssh from iPad with external keyboard and Emacs?
Prompt is generally considered to be the best (or at least among the best) SSH clients for iOS. I've never used it specifically for emacs (as I don't use emacs) but I've never seen it send strange extra characters, even when sending control characters to, say, nano.

Edit: Prompt version 1.3.2 now has a feature where you can use the Escape key as a Meta key.