It comes down to business models.
Holiday Inn are part of Intercontinental Hotel Group (IHG hotels and Resorts). They're a British multinational listed on both the London Stock Exchange and the New York Stock Exchange.
Their Holiday Inn hotels operate on a franchise basis.
What seems to be happening is their franchisees are eager to get contracts from the Home Office to house migrants. Especially as the Home Office aka British taxpayers will pay for wear and tear and refurbishment.
Franchisees are required by IHG to refurbish the hotel at the end of their lease. So if they've got a year to go on the lease it's a no-brainer for the franchisee to enter a migrant contract with the govt and get the taxpayer to pay for the refurbishment. Thus far there has been no interference from their parent company, who appear to be seeing full hotel bookings but not the accompanying reputational damage.
Premier Inn are part of Whitbread Plc, a hotel group founded in 1742 by Samuel Whitbread. They too are listed on the London Stock Exchange.
They do not operate a franchise system, instead all their hotels are run from their headquarters in Houghton Regis. The decision makers at Premier Inn and Whitbread are careful to guard the reputation of their hotels and have thus far avoided entangling themselves in the circus that comes with housing migrants.
This whole saga illustrates the downsides of the franchise model; franchisees are extremely short-termist in their thinking.