It's not necessarily a particularly weak option - sure, it would have been better for her if they accepted the deal, but this is probably about as good as it could be for both sides.
The Marlinists get their independence recognised, with all that entails (though they'll be fine, I think). The Empire gets an agreement that they won't be a safe haven or funder for further neo-Marlinists - which they might otherwise end up becoming in a generation or so, and was probably the main motivation for the protectorate approach - and can potentially attract them back individually through the resettlement scheme (which does of course require some reduction in obvious suppression of Marlinism within the Empire) without having to take risky military action or try to maintain a shaky protectorate, and also potentially it provides a safety valve for future Marlinist unrest within the Empire if the resettlement options work both ways.
It won't be completely straightforward, but it also fits in with ALD's previous preference for "soft" power and cooperation to build coalitions or at least influence with non-Imperial powers. (Compare with her approach via the Blue Star Line to Colonia)