"why shouldn't some councils be allowed to start off their meetings with prayer if they so wish..."
Why not indeed? Except that councils are made up of several people, and if some councillors objected to prayer for whatever reason, what would the new regulations mean for them? If my own past experience (not as a councillor, of course, but in the Scout movement which also has or had a large element of communal prayer) is anything to go by, it will mean sitting around in an awkward, embarrassed silence, whilst everyone else around prays for some length of time that could be anything from a few seconds to several minutes. By any measure, delaying the meeting for a prayer is a waste of time, and yet presumably if the "council" decides to hold prayer, this is an imposition on those who do not wish to pray.
No, the dictating, if any, is being done by those who would insist on holding prayer as a formal part of the meeting. It is absolutely not dictatorial to say "You know what, if you want to pray then you can do so privately, and let's spend the meeting time on actual local politics."