The wording here confuses me a little - I'm going to assume you mean that the employee met the 1,000 hours of service required to enter the plan in one year, but has not and is not expected to complete 1,000 hours of service in any later year. Otherwise your post does not make sense.
Since the employee has met the plan's eligibility requirements, they will continue to be a participant for as long as they are an employee, and will be non-excludable for purposes of the coverage and nondiscrimination tests. So they have to receive whatever contributions are necessary to satisfy those tests. They could be required to receive a top heavy minimum contribution, too.
Even if they never attain 2 years of vesting service, they could still become vested if they reach the plan's normal retirement age, or if the plan terminates.
The one-time irrevocable waiver of participation would not be of any help in this case, as it a) must be executed before the employee first becomes eligible in any plan of the employer, and b) does not get you a free pass on coverage; the employee who waived participation is treated as non-excludable and not benefiting in the coverage test.
This situation could have been avoided by designing the plan with the 2-year eligibility rule, but it is too late for that now.