Btw, I am applying for M.Arch I programs. 

i dont see why not having the right bachelor background will be an issue.  Part of the point of the masters degree program is for those coming from a different background so they dont have to redo a bachelors degree. 

It sounds like that instructors letter wont necessarily help you or anything, but i doubt it will hurt you.  It would be pretty vindictive to agree to write a letter of recommendation just to say negative things.  I'd say if you have one or 2 that are personal and strong letters, and then 1 or 2 others that are general, it shouldnt be a problem or hurt you at most schools.  Obviously, use the ones you feel would be strongest and only use the others if a certain program requires you to submit a specific number.

where are you applying?  Some schools i imagine might put more stock in letters of recommendation than others

It might be vindictive, but many people will do it anyway (it happened to me).

My advice would be trust but verify.  Add one more school to the list of those that you apply to and when he gives you your letter, use that school as your verify option.  Open the letter he gives you for that school to see what he has to say, with the understanding that he will more than likely write one letter for all the applications.  It's not totally foolproof, but that way you can get a sense of what he has to say and pull the other letters if he is clearly negative.

Best luck.

Thank you for your advice. @marmkid I am applying to Columbia, GSD, Michigan, Yale, and Rice. 

Or just keep being a loser, yo!

I wouldnt take to heart what someone who calls himself HandsunCa$hMoneyYo has to say, with ending comments like that

I think most M.Arch programs ask for letters of recommendations.  Chances are, not every applicant has a personal connection to that particular school.  A school wont reject you because you arent buddies with an alum or a professor there.  It obviously will help you if you had that personal connection, but its not necessary.  Treat the letters of recommendation for what they are, pieces of the application process.  Meet their requirements, and the better the recommendation, the better it will look.  If they are just all generic general letters of recommendation, then they wont help you, but if your other stuff is up to their standards, it shouldnt be held against you too much.

Unless we are to believe that anyone who gets accepted to an M.Arch program knows someone at that school already?  I find that unlikely

Also, why would you stay in a program you are not interested in?  I agree maybe finishing the semester or the year, but to stay and complete the program when you know its not for you is just a waste of time and money.  Goals can change.  Staying in a program just to get a letter of recommendation makes absolutely no sense to me

He was being honest, and probably accurate, given your description of your situation.  He's not telling you "forget it," but instead "you have an uphill battle ahead of you at this point."  My strong hunch is that he'll write the best letter he can in these very limited circumstances.

Be realistic.  If you've only been in the program for two months, what kind of recommendation letter could anyone write beyond a "general" one?   You just started, and nobody knows one another yet.  He's got eight whole weeks on which to base a letter describing you and your work.

Students ask me for recommendations frequently.  Some of them may have done reasonably well in my class, but have never been to office hours, and we've never even had a conversation.  I will usually write for them, but it will be "general"-- describing their work in my class over that last three months, and that's it.  What other kind of letter could I write and still be honest?

Much better to ask teachers / employers who have known you and your work for a longer time.  Sometimes, everyone knows, young students don't have three recommenders in that category, and must ask newer instructors, as you've done.  Those letters are usually polite, short, and "general" by necessity.  It's not very helpful to admissions committees, but it's not unusual.