Always a dilemma for women runners: we want to get out and enjoy the solitude of running, yet also have the safety issues to worry about. Like you, I don't want to carry something that could as easily be used on me as by me--pepper spray or weapons.
And I can't say I've resolved this issue to my satisfaction. I live in an urban area. There's a trail I used to enjoy running in my area and have stopped running it alone since a woman was attacked in broad daylight on that trail, despite its frequent use.
But a few things: I carry a cell phone with gps activated when running alone, keep alert to my surroundings and trust my gut feelings. I don't under any circumstances run w/ headphones.
Also it's good to look confident, not in doubt about where you're going. If you're running, this shouldn't be a problem but consider that if you're in an unfamiliar area, you might at least want to look over a trail map before you start and have a planned direction you're going to take. If you know others who run in the area you're considering, get their views about which trails are relatively safe and which to avoid.
Although it's no guarantee, I prefer to run earlier rather than later in the day. There are usually other runners, hikers, and such earlier, while later in the afternoon and evening, things get pretty isolated.
I remember hearing somewhere--forget where--about a woman who pretended to be talking on her cell phone when she saw someone she didn't trust. The idea was to give the impression that she was on the phone w/ someone who could help her, should the need arise. Haven't used that strategy myself, so I don't know how effective it would be, but apparently the woman using this method felt it helped.
While it's not for everyone, if you're able to get a dog to run with you, that might be another option. Having a large dog would likely be a deterrent in itself.
Just a few thoughts--and again don't feel I have this resolved... sometimes I find myself feeling outraged that I even need to worry about my safety: those intent on harassing runners should be the ones worried about their safety. But reality is what it is, and we need to strike a balance: not live in fear, but recognize the need to keep alert for potential problems.