This may or may not be the case, insofar as an organisation can be said to have a position on a vague notion.
As per the article, rms is seeking that:
"Publicly take back Microsoft's attacks on copyleft made in the 2000s. Ballmer called the GPL a "cancer"."
I suspect rms doesn't care terribly much if MS were 'against all things open source' since no one really did, or does, know what that might mean.
When someone in a marketing team of a company sends a message, they usually speak for the company, not for themself, except otherwise explicitly stated. So indeed, we can't expect a huge company like Microsoft have a uniform opinion on all things, but Microsoft as an entity stills sends a more or less coherent message if they take care of their communication.
And I would not blame someone understanding a statement from Ballmer for Microsoft's official stand if the statement was made when he was the head of the company and the company did not issue an apology or a clarification after the fact.
So, at the time Ballmer was a) definitely talking about free software by mentioning GPL, and b) probably not particularly interested in, or aware of, the split by the 'open source' proponents.
