Genocide should work as a definition even if the genus consists of just one individual, I'd think. (Although this could be seen as a mitigating factor if said genus reproduces sexually and thus is going to be extinct after this generation anyway.

)
If it is indeed some kind of single consciousness out of many, then is the Link not responsible for the Link's actions and decisions? Is the Link as a gestalt not then a valid military target?
Quite possibly. Then again, it's currently good manners
not to try and assassinate the real culprits even in times of war, but to only kill, hurt and maim their underlings and subjects of varying degrees of guilt. The explicit aim of coalition forces to assassinate Saddam in the two recent wars with him was somewhat out of line with established US doctrine and commitments in that respect.
OTOH, guilt of war could easily be extended to any number of underlings, subjects and bystanders, as was done in WWII where civilian populations were explicitly considered valid targets by the various parties - both in terms of "collective guilt" and in the concrete sense of each of them contributing to the war effort, however indirectly.
How did they obtain Bashir's intimate knowledge of the people he's been working with for five years?
A good question - but then again, in "Heart of Stone" Odo was in no way amazed that the Founder imitating Kira had in-depth information on DS9 events and happenstances. As in
really in-depth, phrases spoken, holodeck mishaps suffered, the works.
We should assume that there were Founder agents on the station constantly at least from the second season on, doing extensive groundwork. Some probably remained till the very last, that is, the evacuation at the end of "Sacrifice of Angels". Whether they were shapeshifters or other operatives is unknown, but I'd be perfectly ready to believe in a Founder or five being present at all times.
OTOH, Dr. Bashir might have been an ideal choice for abduction, as he was known to be somewhat detached from the community by his irritating mannerisms and sheer snobistry (both probably conscious choices, to better hide the dirty genetic engineering secret he harbored). Few people on the station probably had an inkling of what he did even when he was himself, professionally or privately speaking. And O'Brien had a good radar for such things in other episodes, but Bashir might have been too fluid a character for even the Chief to fully grasp.
Timo Saloniemi