So I know that you can make a worker have a certain pheromone. Is there a way to make it have the harvester pheremone easier? At this rate it'll end up being a scout which I do NOT want.

The throdama won't turn into the morph when it completes the pheromone. The pheromone can be used on a pregnant female to change the unborn baby into a morph. Throdamas that are born as workers will always be workers. This part of the beast codex describes the process in greater detail.

I get what you mean, I think there's an element of luck involved. If you explore islands with a lot of resources, you make a worker who produces harvester pheremones, but I think they're difficult to make because most of the time you'll have explored 20 islands before having collected all the resources. Good luck!