I don't think it's inadvisable. I think most guys masturbate at a few different levels of hardness. I know I start stroking before I'm 100% hard. And when I'm trying to go for a long time I might let myself soften up for a bit while still stroking. But I'm 100% hard when I cum, and I'd say I'm 100% hard for at least 90% of the time I'm masturbating. I don't really know, but I feel like that's typical.
What is uncomfortable about it? Have you tried different techniques that you can use while fully hard?
I know that there are some people who can kind of crack the ligament in their penis when they have an erection. Seems like that would be a bad thing to practice, but I can imagine if there is that kind of tension in the ligament then it could make full erections painful. Might be worth talking to a urologist about it.