The problem isn't that Bubblestrat exists. The problem is that when you take the gym down to 0, the game doesn't allow you to put a defender, and instead lets some jerk who didn't do anything sneak in before you just b/c he had nothing better to do than sit there and click on the gym over and over.
Or even worse, like in my area, a botter/hacker will immediately take it over within 3 seconds probably while they're fast asleep dreaming about all the coins they're going to get. At least with the first situation someone actually had to do a minor amount of work walking to the gym.
The real tragedy is there are at least 10 EASY ways to fix this issue once and for all. But here we are, no fix in sight