The problem here is that the {'e' vImaS} is too far away from the {tlhIngan Hol vIghoj}, so that it sounds like {tlhIngan Hol vIghoj} is a statement of fact, not a preference. One is inclined to interpret this literally as "I learn Klingon; I prefer that it replaces that I learn Vulcan" (i.e., you're learning Klingon, and you prefer that this was instead of Vulcan, maybe rather than instead of something else like Romulan or something). It's very confusing.

Since I knew the meaning you were going for, you want the sentence to be interpreted like this: "I prefer that: I learn Klingon; it replaces that I learn Vulcan". And I think it can mean that in retrospect, but the fact that one has to think about it should tell you that the construction is confusing. It's a "hindsight" sentence.

Why don't you just use the noun form of {'e' qa'}? {tlhIngan Hol vIghoj 'e' vImaS; vulqangan Hol ('e') qa'} "I prefer that I learn Klingon; it replaces Vulcan". Here, it's clear what {vulqangan Hol} is replacing, since {tlhIngan Hol} is the only other noun explicitly in the sentence.