I've always used freebase Rue/Harmala extract in a capsule for oral administration. It absorbs just fine, works fine, i see no reason to use hcl personally. I can use the freebase orally, or smoke it, use it sublingually or snort it, so i go for freebase. Now freebase DMT on the other hand, apparently doesn't absorb as well when consumed orally compared to a salt form, but freebase Harmalas work just fine.
I also consume Rue seed powder in capsules, i found that roasting the seeds first, then powdering and encapsulating, makes it easier on the gut compared to raw Rue seed powder capsules.