I haven't read the axios article but all the questions you asked were answered in the NYT article I read about it this morning.
* Its not disputed that he did earn money playing minor league baseball for $25/wk a couple years prior to the Olympics.
* The IOC rules stated that he could lose his medals for this, but there's only a 30 day window to enforce the rule. The IOC enforced this rule "the next year." I'm not sure if this was enforced unevenly, but there are insinuations that this was due to his race.
* In 1982, the IOC, under pressure, re-instated him as "Co-winner" of the medals to appease critics. This did not appease them.