Maybe the club don't think Agger is good/fit enough for the money he's on, or perhaps the money he'd demand for a new contract? At 27 with two years left on his current deal, we're also never again going to be able to demand anything like what man city are reportedly offering at the moment.
I don't want to see him go, I think he's a class act and it's not just replacing him, it's getting a replacement to develop the sort of partnership and understanding he has with both Skrtel and Carragher, which can't be done overnight. However perhaps the club see the alternative to selling him now for £20m+ as keeping an injury-prone player on big wages who'll go for a derisory amount or even nothing in a couple of years.
If we throw big money to keep him and he continues to suffer regularly from injuries, rarely plays and gets replaced anyway, the club will be seen as being reckless or overly sentimental with contracts.
I thought Kenny should've got another season here but he went because the club knew he wasn't a long-term oprtion. Maybe they feel the same about players like Agger, no matter how talented or adhered to by the fans they are.