The economist thinks PPP's best interest is to stick with the PPP (going by MS's analysis as I didnt read it yet), however the economist also thinks Musharraf is a mistake as far as the west as well as the people of Pakistan is concerned.
The two opinions are not irreconcilable. The article simply states that the PPP's own interests (preserving Zardari, limiting opportunities for the PML to score points at the PPP's cost) are better served by siding with Musharraf than against.
If Musharraf is impeached, it will end with Nawaz looking like a stronger leader, which is bad for the PPP at the next election.