I only use DyeTrees because I wanted only that functionality (Don't use Project Red either). By merging crystals in, and not giving config options, you are going to lose part of your audience (As well as gain an audience for the "magic" mod).
If you want to do a magic mod, go for it. IF you want to move crystals out of geostrata, do it. If you want to remake DyeTrees into said magic mod, do it. If you don't want to add config options, don't.
If you are intent on getting rid of "simple" (Read: in functionality) mod and remaking it into a complex mod, then you should give the code to someone so they can maintain it. I won't use your magic mod just for the trees, or just for the crystals... especially without configs to disable one or the other.
Just my 2 cents. I don't expect anyone to agree.