The short answer is yes, you can "un-participate" an employee who has not met the eligibility requirements (or by excluding the employee by classification), even if you let them participate in the plan when you had less restrictive requirements. There is no protected right to continued participation.
From the 2017 EOB (Ch 2, Section VI, Part E)
If you don't want to exclude current participants who have not met the new eligibility requirements, simply make the amendment prospective. Keep in mind that this could create a discrimination problem if it favors HCEs.
I hope that helps.