Its not a thought crime, its a crime crime.
Second, it clearly wasn't against the law because they dropped the charges and gave her a settlement.
Third, just because something is against the law doesn't mean that you shouldn't have the right to say it. The law does not dictate morality.
If the parliament passed a law saying you cannot criticize them, would you say well it is the law and as such it isn't a violation of free speech? Would you call somebody doing that a criminal?
Fourth, the police literally said "You’ve said you’ve been engaging in prayer, which is the offense.". Meaning the offense was literally her thinking. If you are not allowed to have wrong think then there is clearly thought crimes.
Why don't you see the difference between free speech and harassment? Your stance undermines free speech by giving it zero responsibility. These are rights hard won by our ancestors and you cheapen them by pretending they're all about some cheap technicality that permits toxic groups to intimidate other people.
If you think that is harassment then this is hopeless. Have a good day.