The PT side of the situation seems a little awkward.
The PJ disciplinary unit had conducted an investigation into the slippery-stair saga in 2005
This mostly concerns Cristóvão, but Amaral was also at the Faro PJ station that night.
http://www.tvi24.iol.pt/sociedade/paulo-pereira-cristovao/ministra-nega-recurso-a-pereira-cristovao-de-pena-aplicada-pela-pjAmaral had been a PJ coordinator under Encarnação in Faro. Then at the beginning of 2006, he got appointed as PJ coordinator for Portimão.
http://www.dn.pt/dossiers/sociedade/caso-maddie/noticias/interior/director-da-pj-so-falou-com-o-ministro-apos-demitir-o-inspector-978454.htmlit's not clear if that was a "sideways" promotion or a real one (leading his own team on a particular turf).
Just a year and a bit later, Madeleine disappears and he's in charge.
Although he was made arguido on 4 May (and only charged sometime in June ish in the Cipriano case), removing him so soon after having been "promoted" might have been a bit awkward.
On the other hand, as the torture trial hadn't yet come to court, let alone the end of the legal road of appeals, he was afforded the presumption of innocence like anyone else, in theory.
Also, while the PJ regulations do include various categories of suspension, they appear to be sanctions for misconduct, and not preventive "gardening leave" pending judicial outcome.
Packing him off to somewhere else yet again would have required a vacancy, which may not have been available, plus perhaps the human aspect of not wanting to uproot his family.
What options did his superiors have at the time: send him back to Faro again? Was anyone else available to head Portimão at short notice?
One issue that I don't quite understand is why the PJ leaks to the media were allowed to go on for so long with no inquiry from above. Was it considered an acceptable alternative form of the slippery-stair treatment? Was the PJ too under-resourced to investigate it?
What does appear clear to me is that the national PJ director eventually did hit the roof in no uncertain terms...