GC is going to be the big hit as you're still going to need to pay for that even in C++ land. I'm not really seeing what you'd get over just C# with a more modern JIT unless you start converting to non-safe C code and doing sneaky c stuff behind the scenes (and I'm sure absolutely nothing will go wrong*).
The webgl stuff is fine to not be bound (I'm assuming it's being converted to js anyway?) but anything running in the plugin better be.