Instead of disabling multiconnect completely on servers such as Hypixel, display a warning message when a user tries to force a protocol version, strongly discouraging usage, but allowing them to accept the ban risk.
This will allow users to test if changes made the mod more friendly with the anticheat, and if no bans are reported for a while, possibly remove the warning.

it might be a better idea to add a config option to decide whether mutliconnect should disable, give you a warning or do nothing at all

Oh, so this is why multiconnect just doesn't seem to do anything at all on Hypixel.