The problem we have is that it is now easier to collect everything than to be selective and this represents a huge risk to security down the line in all kinds of ways. You could say our data footprints have become a form of pollution. To mitigate we need to flip it and make non-collection the default - e.g. introduce strict regulations around destroying non-critical information with a very high bar for even temporary storage and anonymisation wherever possible.
Do we just forgo all those benefits because of the risk of abuse or data compromise, by any entity anywhere down the line?
Or do we try to figure out the right checks, both in practices and law, to maximize the benefit and minimize the risks? I'm for that iterative discovery of the right balance. And, I think a for-profit company operating under the microscope of consumer/journalist/regulator scrutiny is more likely to find the optimal tradeoffs than a compulsory state collection program, or other solely bureaucratic and legislative processes.
There are real potential abuses of privacy, but we shouldn't let those scare us into failing to progress. The fact is, you leave your genetic information everywhere you go. If any restaurant wanted to get into the DNA collection business, they would never run out of material. In the near future, I wouldn't be surprised if some people argued that any genetic material left at their business was their rightful property, and since you made no effort to hide the fact that you were eating off that particular fork, they shouldn't have to avert their eyes from your DNA or deny its association with you. Perhaps on your next visit to any chain restaurant, they could suggest a menu more appropriate to your specific health needs.
More to the point, it's absolutely necessary to research this stuff. The more samples we can get out there, by whatever means necessary, the better. This kind of research will absolutely save lives, and in no small portion.
It's good to keep the security implications in perspective. However, if privacy concerns held back or halted basic research on biology, they would do more damage from voluntary and legislative protections than they are capable of doing by creating advertising profiles.
There is also an important cultural aspect that makes certain behaviours abhorrent/unacceptable that would need to be tapped into.
Research is a legitimate and beneficial activity that you would therefore expect to be licensed and controlled.