With that said, I see two options:
1) Keep running things the same as they have been (set plays for jumps shots and ISOs) neutralizing Lowry's positives,
2) Change the way the team plays on offense (i.e. more ball movement and off ball movement combined with more freedom for Lowry to punch and kick) and playing to Lowry's strengths,
If they go 1) then one of Gay or DD likely needs to go unless they can start hitting 3 pointers curling off screens or off pull ups in ISO.
If they go 2) then one of Gay or DD likely needs to go unless they can start hitting 3's in catch and shoot situations.
Personally, I like 2) much better for everyone. I don't think DD and Gay have any chance of making 3's in the situations the offense currently places them in. I don't think the chances are high of them hitting 3s consistently in catch and shoot situations but it is better than coming off screens or pull ups in ISO.
Everyone in the NBA is talented. The job of the NBA coach is to maximize his talent. I think taking the shackles off Lowry and showing faith and trust in him is the only way to figure out what the Raptors have in him and for the Raptors to succeed to the best of their ability. In doing that I guarantee you get a happier Lowry who is likely to totally listen and buy in to the other side of the ball (making the assumption he has not, as many here have). I am not implying this is right. But think about any profession where people are asked to do things outside their comfort zone - they get their back up, it is human nature for the majority.