I do not think any exchange can decide not to accept bitcoin because it will have side effect on the exchange, it is true that the transparent bitcoin blockchain helps in adoption but exchanges can decide to accept only on-chain transactions if they want transparency. Even, in a lightning network payment, only what is most transparent is when opening and closing a channel, lightning payment transaction is not also recorded on blockchain.
You are right if any exchange did get rid of Bitcoin because of silent payments being implemented they would be giving up >50% of their revenue. Exchanges know that altcoins are generating them money only temporary but the long term is Bitcoin. If governments start requiring exchanges to ban any cryptocurrency with privacy features then P2P exchanges will become more prominent and if you ask me I think that will be a good thing because it encourages privacy and usually means people are not going to be using the web wallets on exchanges.