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Pick the Discrete Math course. Really.
Consider this: first of all. there is plenty of software engineering to be done that doesn't require mathematics at all (web development, administrative systems, etc.). Second, for the jobs that require math from your second category (i.e., calculus and linear algebra), you almost always require the first category as well, lest you want to become one of those scientists who write unmaintainable scientist-code
Background: I have an MSc in Computer Science (we don't have a major/minor system in The Netherlands) and I've always had a strong interest in mathematics, so I'm not afraid of either topic. I currently develop software for scientific applications in various application areas, where both these fields of mathematics are very important. My job is relatively rare compared to what most of my former uni-mates are doing. Most people I know have jobs which require algorithmic knowledge, but not calculus or linear algebra.