We know that The Doctor's "death" (or perceived death) was a fixed point in time. But because The Doctor travels through time this does not mean that his enemies should not expect to see him before or after that date! The attempt to kill him was to end his timeline and prevent something from happening in his future (the question "Doctor who?" being answered). The Doctor evaded this by tricking the Silence into believing they had succeeded.
Time travel isn't the sole property of the Timelords anymore. The Daleks have messed about with time, travelling through time corridors and using other technology that alters the flow of time. Then you've got the "cheap and nasty" vortex manipulators used by various individuals. Quite a number of the doctor's enemies that formed the alliance and the plan to imprison him were among the races known to have travelled through time and across dimensions, so it is possible they already knew about the date of The Doctor's "death".
Even though his "death" was established and the plan of The Silence a seeming success, The Doctor's timeline/life would still play out across all the times he travelled to, foiling dastardly plans along the way. So to answer your question Why imprison the Doctor? - it makes sense that these enemies, knowing his death is inevitable, would be happy to just put him out of their way in the meantime. And though you are right, he is known for escaping tricky situations, this was an all-out effort, coordinated by an alliance of enemies, creating what they genuinely believed was an inescapable prison. And you have to admit, the way he got out of it was pretty hokey.
Remember that the time travel element of the show means that, unless events in an episode make up part of an established sequence of events, we can't really be sure if one plan was hatched before or after another. Even though 'The Pandorica Opens' came before the story involving his death, the events could be considered to have come after.