This has been suggested as a potential area for abuse, here actually:
http://www.fantasyflightgames.com/edge_foros_discusion.asp?efid=179&efcid=3&efidt=530611&efpag=0
certainly some of the things covered are so unspecificly written that they certainly can be, which has been covered before.
But in general it is potentially game breaking, and how do you continue to use it without it dominating the game, alternatively how do you control the options without resorting to the same tired 'team on it's own with no support' trope each time.
Should players even have access to the strategic level of play, not so much that they can't advise their superiors but in general, there are entire castes of people set to religiously maintaining strategic line up of crusade.
1. Anticipate, a difficult job, there's a lot in there but when you are making a mission, you can split out what areas of resource are available. However some resources are fairly ubiquitous, the Navy for instance (unless the Astartes are ferrying the team around) and that's perhaps enough for they cause serious problems for you.
2. Time, a lot of Deathwatch missions are last minute, time limit missions, you can have that X you require but it'll take X hours (or even days). Overused though, this may seems like a cop out. Plus, perhaps arranging it may take time it's self. Those astartes are useful but do you have time to arrange carefully planned attack and negotiate with their own Captain.