Yeah, at this point the parserWordCompletion.pl macro will not work with MathQuill. That macro uses the original text input which is hidden when MathQuill is used. This is a problem where per-response disabling of MathQuill would be advisable. I posted a patch to WeBWorK on Github (see https://github.com/openwebwork/webwork2/issues/1155) that makes this possible. You need server access to apply the patch though. Se the instructions in that issue.
Eventually I would like to see macros/contexts for which MathQuill doesn't work (like parserWordCompletion.pl where MathQuill doesn't even really make sense) automatically disable MathQuill for those answers.