I went Light Side when I came across this quest. The reason that choosing Jaxo over the 300 is kind of a simple thing when you break it down.
Ask yourself, will you allow 300 people to die for someone you know or save those innocent 300 for someone that knew what their job entailed.
If your angry that you had to make such a touching chose I suggest you never play Fable III because right at the start you'll be posed with such a question.
In the end though, if you did get the Dark Side points and your just angry that you have taint on your toon then I'm sorry, but that just means you'll need to do an extra flashpoint or something to gain that lost points due to your choice.
In my personal option, the devs and story writes did a great job with the Trooper story line. I didn't like the ending, but I'm not saying anymore to that effect as you will all have to experience that yourselves! All-in-all, enjoy the game!