My bad, I did quickly browse the OP, but apparently not attentively enough. I'm off work now, so I've got a bit more time.
That being said, with all due respect: that's bullshit. The support person just took the easy way out because they didn't want to look into it precisely, but editing this .conf file has been mentioned by Rioters themselves multiple times on these boards. It's not official/supported, as in, if you mess up, it's your own problem to solve (but it isn't hard, just delete the file, that restores the settings to default), but it's not bannable.
https://www.reddit.com/r/leagueoflegends/comments/9aomaj/if_you_dont_know_you_can_increase_minimap_size/e4ww0uk/ Multiple people on reddit saying the same thing as me.
https://www.reddit.com/r/leagueoflegends/comments/a4vsk5/psa_make_your_persistedsettingsjson_readonly_if/ Thread on how to tinker with the file, no one mentioning anything about a ban or any other kind of punishment.
https://boards.na.leagueoflegends.com/en/c/gameplay-balance/ThE0Zdzh-gamecfg?comment=0001 another guy on these boards saying yet the same thing again.
You even got a tweet from the official Riot Support account, from just a couple weeks ago!! : https://twitter.com/RiotSupport/status/1156318291792748544
(Also, technically, Riot reserves the right to ban you at will. They don't need any justification at all, if they want, they can. Yeah, modern EULAs are shitty. But this won't be the trigger.)
Now, it's your account, do what you want. But I'm pretty sure that's safe.