The court could have allowed each county to operate in good faith in choosing any counting method that reflected voter intent,
Election procedures are explicitly a matter of state law, unless the state delegates that authority to the counties or even individual towns. Specifically so two people producing identical ballots aren't treated as having different votes depending on which town they are from. You apparently support letting each county make up it's own methods so long as those methods sound reasonable?
and let the count proceed for a couple more weeks without damage to the winner.
You don't seem to understand the timeline here, or else believe that all election deadlines should have been ignored and deemed unenforceable until when? Until no candidate wants to recount any part of any state under any new standard they can come up with? Until a count was arrived at where Gore would win?
Each state has to produce paperwork officially establishing the slate of electors at least 6 days before the meeting of electors (in 2000 this would be 12/12). The meeting of electors is federally mandated to happen on the 1st Monday after the 2nd Wednesday of December (in 2000 this would be 12/18). Electoral votes are required to be in the hands of Congress by the 4th Wednesday of December (in 2000 this would be 12/27). Congress then officially reviews the vote (and also votes if no candidate hits the required number of electoral votes) on Jan 6, and the current President's term ends at noon on Jan 20.
Two weeks from 12/12 (the SCOTUS decision) is literally the day before the electoral votes have to be in the hands of Congress, eight days after the electoral votes was supposed to have already happened, and two weeks after the state government is supposed to produce the official paperwork about who the slate of electors is.
The absolute best case for Florida doing another manual recount in 2000 would be if they could have done a manual recount of all legally cast votes statewide, but there was only a 4 day window to complete that in from the point that the recount Bush requested an injunction against was called for. From Friday to Tuesday to establish what standards are used to evaluate votes, recount everything, have it completed and the results certified by the state. That...wasn't going to happen any way you cut it.
The first round of Florida recounts were entirely in line with both Florida and federal law, aside from running well beyond state deadlines for their completion and the Florida Supreme Court extending those deadlines (which also got vacated by SCOTUS - apparently changing clear deadlines set in law is less "interpreting the law" and more making it up from scratch to serve your agenda).
Bush's injunction and the recount being killed basically saved us from SCOTUS having to answer questions like "what happens if a state fails to approve a slate of electors by the deadline?", "what happens if a state fails to approve a slate of electors before the day the electoral vote happens?" or even "what happens if a state hasn't supplied the electoral votes by the day they are supposed to be in the hands of Congress?" I doubt you would have liked SCOTUS' answers to any of those questions either, because they probably wouldn't have involved Florida's electoral votes counting at all, and probably would have led to the House voting whether it would be Bush, Gore, or whoever Barbara Lett-Simmons (faithless elector for DC, who abstained in protest of DC not having Congressional representation, but might not have in this scenario) might have voted for in this scenario as no candidate would have hit the minimum number of electoral votes if Florida had no slate of electors by the required date (12/12) and federal election deadlines are enforceable at all.