I do sometimes use some of the large web based cruise agencies to book my cruises and have always received good service ( and OBC and other perks I would not have had otherwise ) and have yet to have a problem.
I have had an agent spend considerable time on a 3-way call with me getting me an upgrade to a Penthouse Suite for only $80 PP more than I had paid for my minisuite after a price drop. And when prices dropped again, they did the same thing to get me additional OBC. So to make a broad statement that these agencies are "not about the service" I don't think is fair. I would bet there are plenty of TAs out there who would not have done as much! I was never impressed with the bricks and mortar TA I had in my hometown, which is why I went to the web agencies to begin with. I am sure there are some very good ones, but they seem to me to be difficult to find.
But, one thing I never do with these agencies is to book via the website. I will call them and speak to an agent to get all the details and then have them book it after all my questions have been answered. With upgrades, etc. I have never lost anything I already had. However, I always CALL the agent, never email a request, and instruct them to CHECK OUT what the possibilities are and let me know what the bottom line is BEFORE making any changes. That way, if anything is not to my benefit I do not have to do it!
The OP e-mailed his TA with a request and she did as he instructed. He really can't blame her if he did not first ask her what would be the outcome of implementing his request.