Most Checkstyle checks can be customized in some way. The exact options (called properties) available vary by check. Each check documents its properties.
So, for instance, MagicNumber has these options. Unfortunately, the properties you are looking for (to allow magic numbers in for loops; to detect only certain individual numbers) are not available.
In such a case, you must write your own check, potentially as a subclass of the check you want to modify.
My personal recommendation is to use the MagicNumber check as-is, and fix all the magic numbers, especially those in for loops. But that's just me. ;-)