There are namespace clashes between Elisp and Common Lisp but the cl package gets round them by appending an asterisk to the repeated names. For instance it implements the Common Lisp version of defun but calls it defun*. The upshot is that there are no namespaces clashes between cl and Elisp and it is quite safe to (require 'cl).
If you want to get rid of the silly warning, customize the variable byte-compiler-warnings.[1] This will turn off the warning when you compile the code. If you distribute the code the warning will probably came back when someone else compiles it. If you don't want this to happen use the code:
(with-no-warnings
(require 'cl))
You can stop the byte compiler warning about any Lisp form in a similar way.[2] It's probably a not good idea in general, but you may be able to justify it in this case.
The code:
(eval-when-compile
(require 'cl))
will get rid of the warning, but you will only be able to use the macros from the package if you do this. Macros are evaluated at compile time and Elisp does not need to know about them at run time. If you only use the macros from any package, not just cl, then it is a good idea to use eval-when-compile as it will stop unnecessary packages loading at run time, both saving memory and making the code faster. But it seems to me that it's a misuse of the function to use it just to avoid a warning. And, of course, if you do want to use any of the functions from cl, you can't use eval-when-compile anyway.
[1] You may need to add (require 'bytecomp) to your .emacs file to get access to this variable.
[2] In theory, anyway, but there's a bug in with-no-warnings that means it doesn't supress some warnings about lexical variables.