Yeah, the namespacing thing is crazy. If its any consolation, it was much, much worse before R 3.0. Originally, packages used to clobber each other's namespaces, which lead to much hilariousness and non-deterministic bugs.

Now those hilarious bugs only happen at the REPL, which is a little better. If these kinds of bugs cause problems for you, i strongly recommend creating packages for your analysis/projects. It doesn't add that much complexity (with devtools, at least) and it does avoid a lot of these problems. Also, R packages require documentation, which is better than many other languages.