It's not clear what you're asking, Sergey.
"I'm going to have to charge you" would be a normal thing to say in this context. And, no, it isn't too much. You need the future form "I'm going to..." because the person hasn't imposed the charge yet. It's also important to add the "have to" because the person is pointing out that they're obliged to do this. This distances the employee from the situation - they're telling you that they're only doing their job and that they're not responsible for the rules.
Does it take a long time to say? No, it doesn't. Remember that English is a stress-timed language, not a syllable-timed language.
"I'm going to charge you"
This sentence has six components, and might take two seconds to say at normal speed.
"I'm going to have to charge you"
This sentence has eight components, but only takes a few milliseconds more to say.
Why? Because natural spoken English reduces, elides and destresses. No native speaker would emphasise all the syllables in that sentence, or even really be aware of them.
In natural speech, "I'm going to have to charge you" would come out as something like this:
"I'm g'n'aftuh charge you"
For a native speaker, this would be barely any longer or more difficult to say that "I'm going to charge you".
Who knows? Maybe in the future, "g'n'aftuh" will take on a life of its own, just as 'gonna' and 'wanna' seem to have done.