'jin' and 'kou' are both valid readings of the same kanji.
The actual funky thing going on here is to note that 'jin' is on'yomi (reading derived from Chinese) while 'kou' is kun'yomi (native Japanese reading). The 'Rai' in 'raijin' is also the on'yomi reading for that respective name. So 'Raijin' would be consistently on'yomi for both kanji. 'Raikou' would be mixing on'yomi and kun'yomi. Such combinations exist, but just aren't as common as straight on'yomi or kun'yomi. And in this case specifically, in practice, nobody ever mixed the two together for 'Raijin' (...until Nutaku :P). Technically viable, but if you say it out loud in reference to this specific deity, you'll get Japanese listeners scratching their head or looking at you wondering what the hell you're talking about.