It's ok to fundamentally disagree with someone and still be civil and polite when speaking with them.

Depends on whar you disagree about. Economic policy, art, media, normal politics ? Sure.

But if the fundamental disagreement is whether certain groups of people deserve basic human rights, then no. Fuck them and everything they stand for, I fucking refuse to be polite or cordial towards people who fundamentally think my girlfriend doesn't deserve the right to exist just because of her innate identity.

Lemmy, and the fediverse, is stronger with diverse people, opinions, communities - even if you disagree with them. Even normies of mainstream political parties you disagree with.

Again, depends on what opinions they are disagreeing on

Downvotes are not a disagree button. Lemmy is not training a personal algorithm to provide a echo chamber, downvotes should mean content is harmful to the community its in.

Yes they are, that's the literal fucking point of upvotes and downvotes, to signal whether you like or dislike something, the appropriate tool to deal with actual harmful content is reporting and blocking.