Roth didn't want Michael's position weakened. Roth wanted Michael out of the way- exterminated! (as evidenced by two assassination attempts followed by an attempt to send him to prison [and Pentangeli in Witness Protection] for a long time.)

I don't think weakening Michael was the goal. Eliminating Michael would weaken and fracture the Corleone empire by default.
But Michael was strong and resilient enough that weakening his position by killing Pentangeli would be repaired in short time, I would imagine.