Back when I was trying to figure out what to do with mine, my idea was to delete the canister and connect the vapor lines with a T fitting. I never got to the point of driving the jeep like that so I cannot tell you 100% but it might cause a check engine light, especially if you have a Leak Detection Pump and detects a leak. In my case I had some other issues with my fuel system so to rule any of that out I re-installed the canister. I found I could put it under the driver seat and its out of the way so I haven't messed with it since.
FYI, I can't have any check engine lights because it has to pass emissions testing where I live.