1. Github could choose to grandfather in those plans and make no changes until those plans expire.
2. Github could offer, or the user could request, a pro-rated refund along with cancellation of the account.
3. Tough luck, those users agreed that Github could unilaterally change the ToS at any time.
They explicitly stated that they won't be doing that: the multipliers go into effect in June for everyone, annual plan or not.
But companies do lots of illegal things, and in general nobody takes them to court over it.
For example, the German Civil Code states:
Section 308 - Prohibited clauses with the possibility of valuation
In standard business terms, the following in particular are ineffective:
[...]
4. (Reservation of the right to modify) the agreement of a right of the user [TL note: this means beneficiary of the terms, eg. party or other subject of the contract] to modify the performance promised or deviate from it, unless the agreement of the modification or deviation reasonably can be expected of the other party to the contract when the interests of the user are taken into account;