Ray,
A lot of paint companies are putting a "matched" primer clause in their paint warranty. In my opinion it has more to do with selling primer than anything else.
Since you were not informed of this special request before you primed, you should not be responsible for a voided paint warranty, so long as you inform the contractor and homeowner and get a waiver in writing. Strip sanding the oil primer would be impractical and very labor intensive, only consider this if the contractor or homeowner is willing to pay for the process. They should also pay if you opt to re-prime the trim.
Benjamin Moore has one of the best paint product lines in the world. An equivalent Ben Moore topcoat would be the best solution.