There is another misuse of St. Thomas, this time on rules.  It is in a section called "Rules and Discernment."

The document quotes Thomas to justify exceptions to"rules," as if the natural law concerning sexual relations did not involve exceptionless negative precepts.  The document lacks a basic understanding of Thomas's view of how rules are applied to particular situations.  

Consider this quote: 304.
It is reductive simply to consider whether or not an individual’s actions correspond to a general law or rule, because that is not enough to discern and ensure full fidelity to God in the concrete life of a human being. I earnestly ask that we always recall a teaching of Saint Thomas Aquinas and learn to incorporate it in our pastoral discernment: “Although there is necessity in the general principles, the more we descend to matters of detail, the more frequently we encounter defects… In matters of action, truth or practical rectitude is not the same for all, as to matters of detail, but only as to the general principles; and where there is the same rectitude in matters of detail, it is not equally known to all… The principle will be found to fail, according as we descend further into detail”.347 It is true that general rules set forth a good which can never be disregarded or neglected, but in their formulation they cannot provide absolutely for all particular situations. At the same time, it must be said that, precisely for that reason, what is part of a practical discernment in particular circumstances cannot be elevated to the level of a rule. That would not only lead to an intolerable casuistry, but would endanger the very values which must be preserved with special care.

347 Summa Theologiae, I-II, q. 94, art. 4.

The document seems to conflate rules such as "You shalt not commit adultery" with rules such as "Return borrowed items."  But consider this statement: "It is true that general rules set forth a good which can never be disregarded or neglected, but in their formulation they cannot provide absolutely for all particular situations."  In this case it seems to confuse rules such as "You shall not commit adultery" or "You shall not murder" with rules such as "Love God," "Help others, "Give alms."   I first thought that the passage was discussing primary and secondary precepts.  But then it seems to be discussing the difference between rules that oblige semper and ad semper and those that oblige semper and not ad semper.  Which does it mean?  And how are either relevant to the issue at hand?

For clarifying these issues, it is might be helpful to look at a good book on Moral Philosophy, such as Ralph McInerny's Ethica Thomistica.