If you are just concerned about resale, then I would say that if you repair the foundation, it would not have much effect on the resale value. Many (many, many) houses around here have foundation problems over time and the difference in the value usually comes from whether or not the owner addresses the problem in a timely manner or allows it go unattended to the point that it causes severe issues with house or would be cost-prohibitive to repair. Unfortunately, your agent is correct that more houses than not have issues around here, so most people expect to read a report regarding the issues with a foundation and are mostly looking to see that the proper repairs were done.
Haveing said that, the thing that flagged me was that you said the structural engineer said it would need minor to moderate repair. Did he say what kind of repairs he thought it needed? Does he explain what he feels is "moderate"? I mean, to some that would be $2k worth of work to others it might be closer to $10k. I would find that out. Also, be aware that if the repairs are too significant, you might be looking at other repairs being necessary (some foundation repairs can damage pipes or sewer lines that would then need to be fixed, or it might cause cosmetic damage to walls, windows, etc).
Having just recently purchased a home (and looking and looking and looking), I know it can be a tiring, frustrating experience, but if you have misgivings, be sure to get the information that will either clear them up or help you decide to move on. A little more time looking could save you headaches in the end.
Best of luck!