What to do with letter of recommendation if you left program unhappily?
My understanding is that you finished your BS 2 years ago, took a year off, entered a PhD program this year but just left due to some dispute about wanting to spend a summer abroad, correct?  (Or maybe you left the PhD program last year?)

Anyway, you should not ask someone to write you a letter of recommendation unless you think they can write you a good one.  If you think your erstwhile advisor thinks well of you and will be supportive, then it makes sense to ask him.  If not, then you should probably stick to letters from your undergrad professors.  

If you apply to one PhD program after having left another, the admissions committee will naturally wonder why you left and if you would have reason to be successful this time around.  Just hearing that you left because of a fight is a big red flag, particularly if it was from a reputable department, so it would be best if you can suitably address this in your application.  You should convince first yourself, then your letter writers, that this is unlikely to be an issue at another department.  Then your letter writers can try to convince the admissions committees on your behalf.