I don't think it will necessarily compromise the sub setup. Subs generally are made to use full range input. It doesn't hurt them. I'd like to know if the Link outs are buffered or just a pass through. If just a pass thru you are getting the same effect as a y connection at the source output jacks. Which may be bad since the input impedance is likely to be only 5 kohm as seen by the source component. Which I suppose is what you mean by compromising the setup.
Subs accepting full range is already a compromise, tho. Subs don't generally need to deal with full range if you have better bass management....