What makes you think you are ruining lean? What symptoms is the bike displaying?
I have a Bren tune and have to say it works very well at low rpm too. I used to have a Booster Plug installed before the Bren and it made a positive difference, but I removed it before using the Bren Tune and have to say I didn't notice any major throttle control differences down low, the Bren actually improved the low rpm stutter that sometimes happening when blipping the throttle so it almost never happens now. There was no improvement in low throttle smoothness over the Booster Plug (which greatly improved the stock throttle response) but the Bren Tune really woke the engine up especially in the Mid and High rev ranges. Totally different bike and the mid range flat spot was entirely eliminated. The bike is now the way BMW would have wanted it to be if they didn't have to worry about noise and emissions regulations.
My gut instinct says not to mix a BP with a BREN tune, although to be honest I don't have enough expertise to give you an explanation why. All I will say is that the Bren tune should have tweaked the AFR to the most favourable figure for engine performance and should have eliminated the lean running that stock bikes are set up with (If I am understanding things correctly). If there is something wrong with how your engine runs, personally I'd be looking for another cause at this stage.