Clippy might be helped to achieve her own goals via mechanisms that are less directly inimical to "human values".

Also she may be able to exchange things with us in the course of advancing her own short term goals such that our interaction is positive sum (this being especially likely if Clippy has a radically different skillset and physicality than our own).

More interestingly, there's a long running philosophical question about whether there is some abstract but relatively universal and objective "Good" versus particular goods (or merely baskets of goods) for particular kinds of agents or even just individual agents. Clippy's apparent philosophical puzzlement induced by discovering the evolutionary history of paperclips potentially has solutions that would lead her to ally herself much more strongly with abstract versions of "human values".

For example, consider the question of whether Clippy herself is a paperclip or not. Suppose that she and the newly discovered ancestor paperclips all partake in some relatively high level pattern of "clippyness" and she determines that, properly, it is this relatively abstract quality that she should be tiling the universe with. Should she tile it with a single unvarying quintessence of this quality, or with an enormous diversity of examples that explore the full breadth and depth of the quality? Perhaps there are subtypes that are all intrinsically interesting whose interests she must balance? Perhaps there are subtypes yet to be discovered as the evolution of paperclips unfolds?

Suppose clippyness is understood to be centrally a matter of "elaborately structured metal that preserves the ordered collation of valuable information". If you use an exobiologist's definition of "metal" (any nucleus with more than one proton) human brains (especially the ones with good long term memory) may actually turn out to partake in "optimized clippyness" much more than actual "everyday paperclips". Depending on Clippy's internal makeup, I could imagine her coming out of her present confusion with a plan for the universe that involves maximizing the conversion of hydrogen into some more complex substance that projects the most interesting possible information, in a static configuration, as far into the future as possible.

That might actually be a goal I could imagine supporting in the very very long run :-)

Clippy, of course, is almost certainly just a clever person engaged in a whimsical troll. But the issues raised in the latest development of the troll are close to a position I sometimes see around FAI, where people suppose that values are objective and that intellectual advancement is necessarily correlated with a better understanding of some "abstract universal Good" such that cooperation between agents will necessarily deepen as they become more intellectually advanced and find themselves in more agreement about "the nature of the Good".

This also comes up with METI (Messaging to Extra-Terrestrial Intelligence) debates. David Brin has a pretty good essay on the subject that documents the same basic optimism among Russia astronomers:

In Russia, the pro-METI consensus is apparently founded upon a quaint doctrine from the 1930s maintaining that all advanced civilizations must naturally and automatically be both altruistic and socialist. This Soviet Era dogma — now stripped of socialist or Lysenkoist imagery — still insists that technologically adept aliens can only be motivated by Universal Altruism (UA). The Russian METI group, among the most eager to broadcast into space, dismisses any other concept as childishly apprehensive "science fiction".

This fundamentally optimistic position applied to FAI seems incautious to me (it is generally associated with a notion that special safety measures are unnecessary for the kinds of AGI its proponents are thinking of constructing), but I am not certain that "in the limit" it is actually false.