I ran into a similar thing and am using boxes to hold excess gold. I turn it into gold plates and then put it in boxes, and then once in a while manually move the plates over to a big array of boxes off on the side, so that the ones by the belt can go back to filling up again. I think it will work fine so long as it all keeps going until recyclers and heating towers are available.
In general, the situation is much like Aquilo, where you produce ice and amonia from the same recipe. The general wisdom is that you end up wanting a way to void either of them, beacuse conditions will change over time and cause you to use one of the outputs more than the other.
A simple way to set up voiding on Lignumis would be to have a special compost heap building that only works on Lignumis and that gets rid of the special local resources: peat, gold ore, and moist stromatolite. It could also potentially manage gold seeds.
Thematically, maybe the building could have gold bacteria as one of its ingredients. The idea would be that there are quiescent native bacteria in there that can consume the native resources.
However it worked, throwing away gold would, in general, just be pretty funny. It would be like Spice on Arakkis: the whole galaxy wants it, but on its home planet, there is way too much of it.