Milton's thesis, derived (with only a little stretching of a point) from Scripture, was that personal compatibility is equally as important to marriage as procreation. (“The end of marriage is in conversation,” as he put it -- which has a delicious double or even treble meaning to the modern ear.) Therefore, if the Church dissolves marriages on the grounds of physical infidelity or inability, then it should also recognize the legitimacy of divorce in cases of intellectual or spiritual incompatibility as well.
To bolster his case -- and the final volumes are largely (increasingly vehement) defences against the counter-barrage of more orthodox pamphleteers -- Milton seeks to show that separation of unlike elements is a scriptural principle and a law of nature. His success or failure in this enterprise I leave to those with the intellectual stamina to wade through all four of the tractates. A good recent book on precisely this aspect of Milton studies is Thomas Luxon's Single Imperfection: Milton, Marriage and Friendship, Pittsburgh: Duquesne University Press, 2005.