I would go out on a limb here and say that the weight of the soil and drainage issues are not relevant. We're talking 100 pcf or so for saturated organic soil and drainage is pretty easily taken care of with geotextiles. 300 psf isn't overly large for a dead load when you note that live loads should not be applied over the same area as it isn't a space that should have traffic during a significant load combination.
Your second point about root damage has more merit but still doesn't seem like a hard problem.
Even if the dead load isn't a problem, the space taken up by a one- to two-meter-deep soil level is going to be significant. (Oh, you were planning on occupying the floor under the tree? Tough.) Also, even if draining the water isn't a problem, pumping all that water up there in the first place doesn't sound cheap.
Your second point about root damage has more merit but still doesn't seem like a hard problem.