It's funny to read an article like the Sunday Times about some government wanting the Commission President to go but not mention once that the only institution that can do this is: the European Parliament.
Article 17.8 of the EU Treaty makes clear that
"The Commission, as a body, shall be responsible to the European Parliament. … the European Parliament may vote on a motion of censure of the Commission"And for a motion of censure to go through (see article 234 of the Treaty on the Functioning of the European Union), it needs a 2/3 majority, after which not only the President has to resign but the Commission "as a body". Which means that even if "Berlin" wanted Juncker out, Merkel would have to organise a large majority of EP members that kicks out the whole Commission - that's pretty unrealistic.
The only other way to get rid of individual Commission members would be a clear breach of integrity (art. 245 TFEU), which would have to be decided by the Court of Justice of the EU.
It's exactly this kind of little detail that makes media reporting about EU matters – in the UK in particular but also elsewhere – create totally unrealistic expectations about what can and what cannot be done, one of the underlying problems that led to the Brexit majority followed by post-referendum chaos.