But don't you see that you are including a high valuation of biodiversity into your definition of benevolent? And benevolent towards who?
Our interests and the interests of various other species are often at odds... and we would generally prefer the aliens to take our side, and if they did, perceive that as benevolence, rather than preference. Whereas if they showed a preference for say, insects, or viruses, such that they destroyed our civilisations, we might infer malice that may or may not be there.
What if the aliens came, identified strongly with humans, and gifted us with all sorts of advanced technologies... a new industrial revolution that met all our needs easily, but required significant changes to the biosphere, such that, for example, species diversity was cut in half.
If an alien species intervened to destroy Kudzu and other aggressive invasive species apart from humans from the face of the earth, would that be benevolent? Not from the point of view of Kudzu.... we would lose a species, but gain in net biodiversity.
On a side note, did you read any of the sequel's to Ender's Game. In it, there is a planet that has a completely homogenous and biosphere, with only one species of grass, of tree, of piglike animal, and one other thing, I can't remember. They live in "balance" but with no diversity. They are all host to the "Descolada" virus which keeps everything in harmony. Surely it is a human aesthetic preference to have diversity for its own sake... perhaps aliens would value fewer, well designed and harmonious moving pieces in their ideal biosphere.