This gets a bit pedantic on the terminology -- sorry for that. I just want to make sure we're clear on what we're talking about. :)
The conversion of Markus to マルクス is technically called transliteration (from trans- [über, um] + litera [Buchstabe] → [umschreiben]), focusing on the letters and written forms. If your focus is on the meaning, then you're looking at translation (from trans- [über, um] + lātus [getragen] → [übertragen, übersetzen]). For names, you'd look for a Japanese name of similar meaning.
German Markus comes from the Latin Marcus, and ultimately derives from Mars (as in, the god of war) + suffix -cus, denoting "(masculine adjective) having that quality". Japanese masculine given names with somewhat-similar derivations might include:
- 軍太郎 (Guntarō)
- 軍之佐 or 軍之助 (Gunnosuke)
- 軍夫 (Isao)
- 軍兵 or 軍平 (Gunpei)
I don't think I've personally ever heard the first two, so they might be archaic -- or maybe just outside my immediate experience. I've heard the third and fourth before; in fact, when I did a homestay in Japan decades ago, my host-nephew was named Gunpei.
Anyway, food for thought. Dealing with names across languages and cultures is always an interesting process. Viel Glück!