Louella, what you mention is THE main reason i think why missions should be revisited and the "engine" or process that assigns them to players redesigned.
There are various different variables that need to be taken into account really:
1) Missions would be much more interesting if there was LESS rats, but with more difficulty and their "payout" was less by direct bounty and more by turning in their dogtags to the authorities. (A-la sleeper?).
2) Missions in "home" regions (that is, the NPC corp owning the station is located within the parent empire sovereignity), can be against enemy factions of any kind, but never portray huge hidden bases or colonies, only "infiltration fleets". The exception to this are pirate factions, which by their very nature could have several smuggling locations or staging bases.
3) Shady or non-ethical objectives could exist in various forms, but such missions should have filters as to which corps can or cannot "issue" said mission. Fed Navy could not send you to fire on Minmatar supply convoys, nor Federation Customs send you to fire on CONCORD.....its just dumb.
In all aspects, the capsuleer is a privateer or hired merc, so the less than "legal" tasks could land on your lap very often, but i don't envision an agent giving you assignments that will put them in a very very bad public light should any of the details be discovered.
Also standings per se should be worked around these points:
a) A Corp has "partners" and "competitors". Partners are strategic alliances or relations (Fed Navy + Fed Intelligence for example), and competitors should be either the enemy factions or coporations that would be negatively affected by your work towards your current agent.
b) Firing on a ship of a given faction, should diminish only very slightly the standings, but to a corp, not the "nation" behind it. IE: firing on a caldari NPC in gallente space should get your Caldari Navy standings into the negative, but not the whole Caldari state.
c) Faction standings should be a "composite" of certain government or nationalistic corporations, and not a straight number out of doing missions for any corp. For example: Standings with the Gallente Federation should be a compound of working for the Fed Navy, Fed Intel Office, Fed Customs, Fed Administration, Senate and President. But if only worked for Roden Shipyards, Creodron and Duvolle...no Empire faction should be upset, only the competitors of said corporations (Kalaakiota, Khanid Innovations, etc).
But well.......it is not going to happen, CCP ginger once mentioned the standing mechanics is soooo complicated and old code that is very difficult to mess with it.