I think there are websites or software to compare gedcom files out there, but my bad idea is to
1. create gedcom files from GRAMPS and Ancestry (make sure you understand the limitations each of those place on creating gedcoms so you're creating comparable files, you may have to do this in chunks)
2. Do the import and GedCompare process (tells you what isn't on wikitree)
3. Copy/Paste the table from GedCompare into Excel for both, and do a vlookup or something to figure out which ones are in GRAMPS but not Ancestry and vice versa
4. Create gedcom from Wikitree, matching up the chunked tree limits to however the gedcoms were created in GRAMPS and Ancestry
5. Import into GRAMPS (assume it has some comparison capability, I haven't used it, but it looks fairly advanced)
6. Import Ancestry gedcom into GRAMPS. Match up whatever was missing from 3 above
7. Import one of those gedcoms into Ancestry (assuming you can do this, don't have an account there either)
now they should be in sync