I don't think it was so much having only one team in the Bay Area so much as the prospect of that only team being stuck in East Oakland and not the more prestigious San Francisco. That would be like having the only LA team be the Angels down in Anaheim instead of Dodger Stadium's pretty central location. Speaking of the Dodgers, a big part of the opposition to letting the Giants move came from them not wanting to lose their most traditional rival. I still don't think they have a problem with having only one team in the Bay Area in the present day. Again, none of the other major pro leagues have an issue with it, so I don't see how MLB is any different.
But the A's wouldn't be "stuck" in Oakland in that scenario. They'd be free to build a stadium anywhere within the market: San Francisco, Santa Clara, San Jose, anywhere in the area. The Giants were TRYING to get a new stadium in 1989 and sold in 1992. (Candlestick was 36 years old and the Coliseum was 26 years old). The A's are only stuck in Oakland NOW because the Giants stayed put and the 1999 type meant the A's couldn't build in Santa Clara/San Jose.
The whole "none of the other sports leagues has a problem with it" isn't valid at all.
NHL - non-traditional market that had a massive deficit in terms of US markets in the 1990s. And the Seals thing didn't work exceptionally well. The Sharks HAVE been very successful as an expansion team and it's largely because they have the best of both worlds: The Sharks were THE only team in San Jose (before the 49ers moved to Santa Clara) and the only one with San Jose in the name... So it's like a Nashville or Columbus situation where you have a loyal fan base from "The only game in town." But the suburbs of San Jose (aka RSN TV territory) are SF/OAK/Sacramento, which are the #4 megalopolis in the country.
NFL - (A) they HAD two Bay Area teams for a long time and are only powerless to stop relocations to open markets unlike MLB can BECAUSE the Oakland owner won a lawsuit with the NFL. (B) Only national TV contracts, no local regional sports network revenues, rendering the topic moot.
NBA - Actually HAS two teams: The Warriors who played in Oakland, now San Francisco; and the Sacramento Kings, who despite SF/OAK and SJ and SAC being listed as three separate markets, are one big TV market for the purposes of regional sports networks, which is where the big sports money comes from.
The Dodgers were definitely against the Giants moving because had it happened, the NL West would have been: Los Angeles, San Diego, Houston (CTZ), Cincinnati (ETZ), Atlanta (ETZ), Tampa (ETZ). Not exactly "West." It would have done damage to their TV revenues to play only 9 road games at 7 pm and all the rest at 4 or 5.