It's actually trivial to prevent from a programming perspective: don't automatically link accounts, and even if they are "linked" (for login purposes), don't import/export personal information from them.
Now, a disclaimer -- I think how Google has approached this is dumb.
But, what if linking that info allows for better UX and features for your customers? At least for the majority. There will always be edge cases, in any feature we as developers ever build... Is it really as simple as "never do that, ever"?
In Google/YouTube/Google+ -- yeah, I think you can make an argument that people expected those accounts to be separate when they made them and G should not have forced them to link them. Bad form. But I honestly can see some cases where that sort of linking can be used positively.
In my humble opinion, the real issue is 1. How google forced the linkages, and before their latest "Pages" feature (which is hard to use even still) didn't allow for a workaround, 2. How long everyone's google and YouTube and android accounts have existed for. You made your YouTube account thinking it was separate. Now it's not, and that's an issue, due to a (correct at the time) assumption you made in the past, and that's not your fault.
It's a shame that this is such a mess. The only Google product I still use is Search these days. They lost my trust over a year ago now.
For me, as a developer and user, the main priority is only one:
Don't cause irreversible consequences.
That's the reason we have the "Are you sure you want to delete this?" dialogue boxes where it matters and "Undo" buttons where it doesn't.
Given the nature of the internet, the developers (especially Google) should know that once you link two accounts/names, you can't unlink them, so preventing accidental linking should be their priority.
This is the same reason I don't support automatic updates that introduce breaking changes, and I rarely even update my apps nowadays. This is also probably the reason I will buy an iPhone next time, even though I strongly oppose their closed-source/walled-garden philosophy - my my personal information and well-being are more important than open source, and at least I'm paying Apple with money, not information.
Fwiw, I made the same decision with my device choice, for the same reasons. I do run my own calendar and contacts server over SSL, to help safeguard things a bit more, as I don't trust Apple all that much either.
Far and away the biggest problem with all of this is that it's not opt-in. None of it. Not even the decision to have a G+ account at all, unless you posit that everyone who signed up an email account a decade ago before "social network" was even a thing.
To then turn around and call it "user error" when some forced integration has undesired consequences is just abominable.
