This seems like the biggest downside I've seen mentioned thus far. Can you (or anyone) offer more detail as to how using Conda resulted in corrupting your Python installation? It it similar to what can happen with game mods, or is there something else going on?
Probably Conda is fine if you just commit to it, but I think the users who got into these messes weren't knowledgable enough to oversee the consequences of their actions.
So you could argue that the problem isn't with conda, but with the users. However, it seems that for naive users the consequences of using conda aren't clear (enough), which can get them into a mess.
I hate to hear that you had a bad experience. If it’s at all possible, please provide something on our issue tracker (github.com/conda/conda) we can replicate and write regression tests against. Help us improve on what we’ve missed.
Using the miniconda installer often helps keep it lightweight too, no need for Anaconda in many use cases.