Take your new Air and run! You're very lucky they're offering to replace it at all - I would've thought since they made you pay for the repair that they had voided the warranty due to liquid damage. As for the two models, totally up to you - do you want the faster processor and SSD? I'd think "yes" is the answer you'd like to say, unless the $300 is a huge issue...
The warranty would've been voided if I decided not to repair through them.
I'll probably go for the faster processor/SSD but I'd rather have a Macbook Pro over that. If anyone could shed some light on different computer type replacements, that would be appreciated.