Consider this situation:
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The PCs are offered a quest to slay a monster that has long troubled a town. They accept the quest and eventually return with the monster's head (or some other proof of success). They are rewarded for their great deed and later leave, continuing on their journey.
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Now, to me this does not seem that different from an assassin that is offered a job, accepts it, and follows through with it. The core rules states that an assassin must be evil because it assumes the assassin will always accept the job - that is, that greed is the ultimate motivation. Yet other motivations can also exist: patriotism, a desire to aid others, etc.
Personally, I find it odd that a game based upon slaying creatures and gaining / taking loot would state that one who makes their livelihood in this manner is intrinsically Evil - or even utterly incapable of being good.
The assassin in the core rules is typically seen as part of some shadowy organization that will always accept any job they have a fair chance of succeeding in performing - irregardless of whom the target happens to be. Yet when I think of assassins I rarely imagine such a guild. Usually I imagine lone hitmen or government agents, the former often unknown except to those 'in the know' and who may accept or decline any offer based on their own (sometimes unpredictable) views. IF they decide to go along with it then they are probably going to request some percentage (at least a quarter, perhaps as much as three quarters, usually half) up front. The latter may be part of an official spy organization within the government, or it may be an elite team of 'special forces' or 'elite guards' that mete out 'justice' as their Lord / Senate / etc sees fit.
The 'shadowy organization' assassin guild bit always struck me as equivalent to a mercenary company, but one that works on an odd individual level or sends in a team - like, say, a party of 4-5 adventurers. In fact, I tend to see mercenary companies as the historical (and modern) equivalent of the 'typical' adventuring party (which, often, is not specifically and completely tied to a single lord or government, as might be expected of a group of knights, a privateer ship, etc).
Thus, I see no problem with having a 'good' assassin, but then I admit I rarely pay much attention to alignment. So long as the 'good' assassin is not in a situation where they are expected to take whatever job is given them, of course, (as would be the case in the instance of a guild member or even an agent for a non-good government) because then their alignment may find itself conflicted with their objective.
If the assassin is part of a guild or an agent for some lord, religion, etc, then it might be best to state that they can only be good if their organization is good, and that they must be within a step of their organization's true alignment. A LN government might hand out assignments that could stray into LE, so a LG assassin would eventually find their AL compromised, but if you follow those two rules above, then the assassin could only be LN, LE, or TN - none of which would be compromised by the occational LE job. Similarly, a NG organization would - by its nature - be quite unlikely to have Evil jobs for its assassins. The jobs may be of any good alignment or occationally a truly neutral alignment, but it won't be calling for a Harold-esque slaying of all children two or younger. Actually, it would be the type of organization that, hearing of such a plan in the works, would send out an assassin to slay the king prior to his making the plan a known command to his guards / army.
So, those are the rules I propose for an assassin that is part of an organization:
1) The assassin can only be good if the true alignment of the organization is Good.
(If the organization is publically known to be NG, but its true alignment is NN, then any assassins working for it cannot be Good, as sooner or later they are likely to get Evil leaning assignments.)
2) The assassin must be within one step of the alignment of their organization.
(The jobs an assassin is likely to get is probably going to be determined by a large degree by the true alignment of their organization. Thus their acts will draw them ever closer to their organizations' true alignment, presuming they fulfill their jobs.)
How do these work for you.