The 2009 agreement with the EU mentioned in the article seems to be the one about the integration of the Internet Explorer (IE) into MS Windows.[1] But it only applied to IE and the commitment was limited to 5 years.[2]
Or is the article referring to something else?
I see no reason why the EU should object to Microsoft's adoption of eBPF as long as MS Defender simply uses the same API that is available to all competitors.
[1] Here is the original text: https://ec.europa.eu/competition/antitrust/cases/dec_docs/39...
[2] See section 4, paragraph 20.