Martino, did you get a written agreement that the council would fit it for free and if so did it mention anything about a security charge.
Secondly have you asked the council for a copy of their policy (under a FOI request if need be) which should clearly state that they have the right to apply a security charge and ask why you were not told this in advance if that is the case.
Councils, going by my own experience, normally supply disability items that they can loan/take back, but their can be grants given by council’s or other bodies for permanent adaptions. It may make a difference if you own the property rather than rent it from the council, which you seem to suggest.
The bottom line is, as always don’t just accept a decision because someone has told you that it is their policy, ask them to prove that is their policy and then decide whether you want to challenge it.