Is there any way to exclude fringe benefits from the definition of compensation used to determine a SEP contribution for employees?

IRS Publication 560, page 4, provides a general (and broad) definition of compensation. One key word is that the employer "can" define it to include their entire list of items (wages, fees, and other). "Can" means there is a choice available to exclude items as long as it's not discriminatory.

So I would say yes, you can exclude fringe benefits. Probably go with "wages and salary".