Hey @Purrsia_Felidae,
Funny you should mention alternative aligners, @epruesse is working on a SINA aligner as we speak, however given the size of your dataset (and assuming your ultimate goal for alignment is to generate a phylogeny), you could try using a SEPP algorithm provided by this plugin:
Of course, we could always use more help, so if you have a bit of Python experience, you could always create some PRs for q2-alignment adding more (or even create your own plugin which does whatever you want).