A message from our CEO about the future of Stack Overflow and Stack Exchange. Read now.
1 of 3

This is a complex situation, and to even attempt a truly thorough answer one would need to know more details than you have provided (though your reticence is understandable). I would begin by saying that in my opinion the main problem is not what you think it is.

My advisor has NO knowledge of the field.

This is the main problem. You're just starting a PhD with someone whom you feel has much less knowledge than you, and accordingly is pushing you into professionally dubious situations. You characterize the situation as that she needs publications and thus making you do the work...without enough understanding that the work you're doing is not mature.

I think you have one of the worst kinds of advisors. It would be less pleasant to have an advisor who is overly intense / unfriendly / borderline abusive, but such an unpleasant advisor would still impart knowledge and experience. There is no reason to stay in a PhD program under your circumstances. I encourage you to very seriously consider transferring to a different PhD program. Based on what you say, the non-academic aspects of your current situation are comfortable enough: that makes it harder to pull the trigger, but it does not make it less of a good idea.

I know I could perhaps learn more with a knowledgeable advisor, but I'm positive I'll learn a lot on my own anyway (perhaps with occasional inputs from other professors from my institution who are active in the field), so it's not like I'm wasting my time completely.

You can remove the word "perhaps." The main thing that makes one PhD program much better than another -- not necessarily in the sense of rankings, but really "better" for any given student there -- is the level of knowledge and expertise of the advisors. I went to one of the top three programs in my field, and every faculty there is a world leader. My former PhD advisor is, truly, one of the world's great living mathematicians, and being guided by him for four years was really priceless. You mention that you are skilled at learning on your own, and I believe you, based on your ability to, at such an early stage of your career, gain expertise in a field beyond that of a faculty member. Learning on your own is also a very important and valuable skill, and I did a lot of that as a student. But you know what? If I had it over again, I would talk to my advisor more: there were times when I spent whole months doggedly figuring something out on my own which one conversation with my advisor would have cleared up. (I now see this happening with my own students sometimes.) Learning on your own and learning from the real luminaries are the two great tastes which taste great together. You're right: you are not wasting your time completely, you're only wasting it relative to what you could be doing. You sound like quite a good student: I think you deserve a better experience.

Let me now address the top-billed question:

How likely are these publications to mar my reputation/CV in the future?

Most academics I know worry about their reputation and standing to a degree that would make most fraternity guys / sorority gals envious. There are very few single events that outright ruin an academic's reputation: these mostly center around academic dishonesty or non-academic crimes (e.g. being truly abusive to a student). If you have published a paper that is subpar, then the way to bounce back is to publish more good papers. And by the way that is what you should do even if you haven't published a subpar paper! If the subpar papers are the ones you did earliest in your career, most people will understand that you wrote them as a young student before you really knew what you are doing.

To my mind, the key worry is not whether your paper is worthless, it's whether it is wrong. Publishing a paper that you know to be critically flawed in a manner that you don't call attention to is a form of academic dishonesty; some would view this as even worse than plagiarism. I would try to avoid publishing such a paper at virtually any cost.

Will people just understand that everyone has had to undergo a similar situation some time in the past and disregard them in favor of better publications? Does everyone have a couple of stains in their record?

It depends on the people, I suppose. I have never been pressured to publish a paper by anyone, but I work in a field (mathematics) with somewhat distinctive cultural norms. But if you're asking whether every academic in your field has been put in your situation: almost certainly not.