I can understand a want to rationalize the designer's choices, but in this case... no. I honestly think both the intro and the adventure is best served by being separated and not used together. It simply is the solution that solves all the issues in one fell swoop.
I really don't feel the same way. The adventure needs multiple skills to survive and finish the adventure. The ability to fight and win is a lesser skill in the adventure but it IS required. I think the intro also works because the rest of the adventure has very little combat and for an average group of D&D players having a bunch of combat first session gets it out of their system and allows them to roleplay for a bit without worrying about when their next fight is going to be.
It obviously depends on the personality of your players(and their characters).
Which is exactly my point. The risk of this happening was the first thing that came to mind when I read the module. Then it took me quite a while to really break down what exactly felt wrong about it (since it is awesome in so many other regards), until it hit me that the intro and the main adventure isn't playing the same game or in the same genre even.
I think I like it precisely BECAUSE it attempts to span multiple genres. It takes the typical adventurers and throws them in a situation they aren't prepared for and forces them to improvise. This is my favorite type of adventure specifically because it makes them players stretch "muscles" they don't normally use. I enjoy running it because it's fun watching the players squirm to figure out what to do in a no-win situation that is really meant for someone with a completely different skill set than they have.
The adventure(for part of it) plays a lot like a Call of Cthulu, Paranoia, or Legend of the 5 Rings adventure where you are often stuck in a situation you can't control and can't really solve and instead need to weather the best you can. I admit, this can be rather frustrating for certain types of players, mind you.
I recall, in particular running a L5R adventure once(using d20) where the PCs had to solve a murder with very little combat. It was made extremely difficult because of the culture in L5R. All of the evidence points to one person being the culprit but that person has high social status and no eyewitnesses will admit to seeing them there and physical evidence isn't allowed in their justice system. So, the PCs need to come up with a way around this by trying fruitlessly to convince anyone to speak against him. When I played it it was a rather fun roleplaying challenge that I got a kick out of. But one of the people playing in our group got so frustrated that he just decided to walk into the palace of the suspect and try to kill him. When he died, he swore he was just going to roll up new characters repeatedly and keep attacking the palace until he won because he was tired of trying to prove it was him. Ironically enough, the real murderer is NOT the one the adventure points to the entire time. He is being framed.
I was having a great time and to this day it was one of the most memorable adventures I've ever played. But to him it was extremely frustrating and he just wanted it to end in any way he could.
I feel that Murder in Baldur's Gate has a similar feeling. For a large part of the adventure, the PCs really CAN'T do anything to solve the adventure short of killing all 3 of the patrons. And given they are all fairly well protected and most PCs are good, that idea may never occur to them. Also, most PCs really don't attempt to solve political problems. I know my current group has not tried to get any of the laws overturned. They feel that laws are beyond their power to affect.
(What I personally think is that the writers got so enamoured with their idea that the PCs are helplessly swept along, that they completely forgot to add DM advice on how to give the PCs agency... but that's just me)
To be completely clear:
I think Murder... is an awesome adventure, but I would never even try to make it work for standard D&D heroes.
I think that a certain subset of "standard D&D heroes" work fine in the adventure. Essentially, any D&D character who has mostly good motivations who wants to help the people of the city the best they can and want to solve the problem the city is having works well. Either that or people who feel the need to solve mysteries and get to the bottom of problems. Which is a large number of adventurers. The only real problem is that these people will likely be frustrated as they are blocked at every turn and roadblocks prevent them from solving things immediately. If the players have patience, however, it can be a fun pay off at the end.
I find that people with selfish motivations can work decently well. The patrons keep offering money to go on missions(though, the adventure fails to tell you who offers what amounts of money...which would be nice to know). These characters might continue blindly helping the patrons ruin the city simply because of the money offered until the city gets so bad that even they should feel the need to stop adding to the chaos and to solve it instead.
The only people it doesn't work with are people who don't care about money and are not good aligned. Like the bard that left my campaign. He felt he was a travelling bard and one city's problems certainly were not his problems and he should get out before it became too bad. Though, in my experience, this is not a typical D&D adventurer's attitude. Most attempt to solve any problems they are presented with. Especially when it happens to a city that considers them to be "The Heroes of the City" like they are after the intro. They feel protective of the city and want to help it out of respect for the people.
I think that the characters are often the lesser barrier to the adventure. The PLAYERS are a much bigger barrier as they are likely to get bored of the lack of combat or frustrated over the lack of progress.