I would suggest changing the rules and allowing Lea to compete in this year's Tony Award; letting her be nominated as Best Actress in a Musical (she would probably lose to Victoria Clark anyway). But a performance this fantastic, rising above her own scandals and drama surrounding the revival, should be recognized in some way.
There are many precedents for Tony rule changes. The most extreme in acting, I believe, was in the mid-fifties when Lotte Lenye was nominated for Threepenny Opera when it was playing off-Broadway at, what is now, the Lucille Lortel. Like Lea, there were ancillary reasons beside just a fantastic performance, but I would think a rule change would be more justifiable than a special award.