Normal. They get used to it. Mine actually run into the spray now.
Anything new is likely to be met with this sort of run-away-now-ask-questions-later reaction. Your tortoise will take a little while to realize its not tortoise death acid spray.
Tidgy did the same when I first sprayed her, ran as if pursued by a pack of hungry tortoise eaters.
Now she loves it and will follow the spray as I move it.
You ARE putting stress on it, but that is okay. Think of how much stress a wild tortoise deals with on a daily basis. Our captive tortoises have a very "cushy" existence in comparison. Studies have shown that some stress once in a while is good for captive wild animals. You don't want chronic stress all day every day with no relief, but a little spritz now and then to get the blood pressure up and get them moving is not a big deal. Plus it desensitizes them to yet another thing.
I figure their reaction to experiencing rain in the wild for the first time would be exactly the same, but soon enough they get used to it. Its the same with all animals (even humans). If I heard a gunshot it would freak me out, but if I were to live in a warzone were gunshots are often heard my reaction would change slowly.