I voted #1, though #4 could also be made to work: we'd just need an alternate way for newcommers to get the rares. (Could be slower, but shouldn't be crippling.)
What if the rare weapons quest was repeatable - with the score required for each new weapon four times the last one (it starts at 500). That would give everyone the handfull of rare weapons to build a rainbow, at least.
And what if rare farms weren't eliminated altogether, just made... rarer? Have some server-side code check each top50 deck. If it's a rare farm decrease the encounter frequency to 5% of the original ... or 1% if it's also made from incompatible pillars. Since many non-rare farms have rares (flying weapon decks have weapons, many many decks have SoG) these would therefore still be obtainable, just not from farms.