I frequently book cruises with discount websites. I have had good and bad experiences. the main downside is that until you get in touch with a TA you like to work with, you are randomly assigned one of their agents. They could be good or bad. The positive is they typically have a main number you call and if you have an urgent issue, any TA can deal with it if your TA is unavailable. Also, read the fine print, some of these agencies do charge booking fees and/or cancellation fees.
I will continue to use discount sites if I get a good price, but if the price is close to the cruise line's price then I just book direct.