I did the Force Recon quest and killed the Order Knights with the Scoia'tael warriors.

Will I still be able to go through the neutral/witcher path? I am already in the beginning of Chapter 3 and I really don't want to reload and lose all the stuff I have done...

No, right now you can still choose any of the three paths. The limiting decision is in 'Gold Rush', and it just removes the possibility of siding later with whichever group you fight. You will always be free to take the neutral option in the end.

Thanks a lot, man. I mean it.

Yeah Force Recon doesn't really affect anything other than which blacksmith you have to use. Because there aren't any survivors or witnesses, the side you fight against doesn't know that you were involved. Yaevinn wasn't present, and Siegfried didn't participate because of his injury.