Ancestry.com gives two possible origins for the surname Malan: 1. French: nickname from Old French malan(t) ‘sore’, ‘ulcer’ (Latin malandria). 2. Czech and Slovak: nickname for a small man, a derivative of malý (see Maly).
In South Africa we trace it back to French Huguenot and Dutch settlers, not Czech ... and I could readily imagine someone wanting to use the ln Malan as a fn, having a girl, and (probably inspired by Melania or just Melanie, which does indeed have a Greek origin) tweaking the ending to make it look fem. Here we'd say mah LAHN ee ah, since we pronounce the ln as mah LAHN.