Sure!
Unchecking the update does not prevent your OS X system from showing you the same update the next time.
In that update window, click on the Safari line, then choose 'Ignore Update' from the Update menu. That _will_ stop that 'annoying' update report for Safari.
As updating Safari also will update your Webkit tools and files for OS X (which some other web browsers also use), you can consider updating Safari, even if you never use it.
Just curious - which browser do you prefer, and have you tried Safari recently? I think it is nearly as fast as Google Chrome, without the additional baggage that Chrome has.