Yes, you are correct.
Couple suggestions :
1. Export a GEDCOM for just a couple of generations and work your full list in small bites
2. Treat matching on the gedcompare as a "reasonable match", so that if there is just no info on the profile to match to other than name and year, no family or spouse or even location, reject it. You are trying to figure out which profiles might be duplicates, but merging later is always an option. I found somewhere a response that mentioned that unmerging a bad match is harder than merging two completed profiles.
3. Keep in mind that "match" ing in GEDCOMpare is just impacting your list of entries on the gedcom, NOT doing any matching/merging on the profiles in question. Its the edit AFTER the match that matters. Dont let the perfect be the enemy of the good.
Lastly, even if it takes a long time, you'll get through your GEDCOM if you just keep going. Don't set your goals on getting it all done, just get something done every time you work it. People have planted entire forests and carved through mountains by themselves, they just kept going.
Hope that helps.