I think you are absolutely correct.
We already experienced two conquests in a row that opponents just donate tons of extra stone by using gems. We destroy a tower, they still keep building new ones and even upgrade tower levels, while we already ran out of stone a long time ago. And that despite the fact, we own a mine and the opponent doesn’t. I know number of members also influences the ability to keep building (more members means more donation of resources), but I honestly don’t expect any team to be able to build new watchtowers with all their builders for more than a couple of days, every team will run out of stone and wisdom eventually, without extra donations on the highest tiers.
I think you make a good point here, it should not be possible to get extra stone in conquest at all. For conquest score you need a lot of stone, especially in top tier. In that layer 5 players having max stone donation are required to build one new watchtower. To upgrade a tower to level 2, you need at least 10 players with max stone donation. So when a lower team is having a lot of towers and can keep building them, it must be done by extra donations, using gems.
A fair conquest should prevent possible extra stone donations. I think wars should be given a little bit more extra, in case of watchtower destruction. Give for example 10% - 25% of the stone as reward to another team for destroying a watchtower. Then at least it is worth attacking opponents.