Well - if we choose to follow tsar's Paul laws, which still were the main laws during Nicholas' reing, then Kirill COULDN'T technically be heir. He was married to his first cousin, which is not (as you have said) permitted in the Orthodox Church; moreover, when there still was a throne Nicholas, the head of the state, never recognised the marriage, so for this two reasons Kirill's son COULDN'T be tsarevich.
But as Belochka stated, this laws were no more effective when the Provisional Government took power.
IMHO, it's a problem of choosing - do the living Romanovs want to continue to follow - among them of course - Paul's law? If so, technically, the hereditary line has estinguished when Alexej died. The don't want to because they are not valid anymore? Well, so Kirill should be considered heir because, as Robert pointed out, there was none else left.
Note that even Michail - if he had survived and all - couldn't be heir according to Paul's laws - his marriage was bnever recognized, and was morganatic. His son was not a Romanov, and all.
I have always thought Paul's laws were too restrictive: i mean, one to be heir should have too many necessary requirements to be "ok". It was inevitable that, sooner or later, the dinasty couldn't have provided someone who could fulfill them perfectly. Here, IMHO, also lies the deep of the tragedy of Alexej's illness - beyond Alexej there was, in that precise moment, NONE ELSE who could really be heir fullfilling the requirement's of Paul's laws.