The only safe way to use emacs wiki code is to audit it first, and el-get can't do that for you.
A robust process for auditing packages is going to be hard to establish. In practice most developers seem to be happy to install any and all updates as long as they're reasonably sure they came from the original author. By using verified upstream source repositories both el-get and MELPA ensure this is the case, as long as one steers clear of libraries originating from the EmacsWiki.
Emacs is no different.
Apt, Yum, etc., require trust in the repository infrastructure and those select few with write access to a given repository. Emacs Wiki requires trust in the entire internet.
And now people realize why I'm a luddite and just keep all my dependencies rolled into my dotfiles repo directly and have done so for years.
1) it's standard emacs
2) although it doesn't have yet it will be able to support digital signatures for packages (as well as other security mechanisms)
As a developer of Emacs packages (it seems to be the only code I've written this year, outside of work) I am sticking with package.
I don't know how much the tips here might be relevant to el-get, I think not very.