It doesn't necessarily imply respect. Calling someone qaH or sir just shows acknowledgement of the addressee's superior station.
It's also more than just agreement. It's an answer to a yes/no question. If your superior told you, Ha'! matlhutlhnIS Come on! We need to drink, you wouldn't agree by saying HISlaH, qaH; you'd say lu', qaH Okay, sir.*
Note also that qaH is gender-neutral, while sir is usually masculine. Whereas in English we might address a woman as madam or ma'am instead of sir, in Klingon she is still qaH. I wonder if this course considers that possibility?