It's always peace of mind to take a course from a dive shop as a good dive shop will ensure you complete your certification, even if your assigned instructor can't finish your course. Most of the instructors from dive shops are also more experienced as they teach more. Student diver will also have better facilities like air conditioning class room, good AV system, better dive gear, safety equipment etc etc...
But bear in mind that not all the instructor attached to dive shops are good instructor. Some just work in a dive shop for a living, not so much because as passion. Teaching courses becomes routine to them, hence the student diver become boring. And small few numbers of instructors which are with famous dive centres become a bit too proud and could be impatient with their student. That will also reduces the fun during the course. Price wise also could be higher.
As for freelance instructor, I'd say that most freelance instructors have a day job. They just do this for passion, because they like to bring the joy of the ever so wonderful underwater world to their student.

Hence the whole course will become fun and exciting as the instructor will ensure the student diver experience the fun as he/she does during diving. I personally know some really good freelance instructors myself, so they can be good also. Price wise, most freelance instructors charge cheaper than dive shops. There is also a saying that freelance instructors seems to be friendly (maybe they work for themselves, need to keep a friendly image

)
We've heard from time to time, stories of MIA instructors after paying certain amount of fees to them. I wouldn't want to go into this but there's always a black sheep in all industries. Freelance instructors may not have all the luxury facilities that a dive shop could have. Worse still some instructors become freelance because no dive shop wouldn't wanna hire them.

Time table arranging could be a hassle if the instructor have a day job...
All of all, the rule of thumb is: Meet as many dive instructor as you can before deciding. Talk to them, ask questions, joke with them. Student - Instructor matching is a very subjective thing, even the best instructor would not be suitable to all. On the other side, even the biggest company will have bad track record. So I personally think it's not so important of where is better to take a dive course. The most important is finding the right instructor.

. Hope helps!
