My take on it. Ymmv.
Well, one interesting thing about D&D is that you usually don't have gaping wounds that keep bleeding from a sword hit or a morningstar bash. It takes a special magical item or feat to allow "continually bleeding" wounds like that. Furthermore, someone down to 1 hp is just as able to do everything, with no penalties to anything, as someone at full hp. So maybe the fact that poisons' ability damage actually has a game effect on an ability, and all which that ability governs, rather than simply putting one closer to disabled/dead/etc., might make a difference. So poison use actually does have a worse effect. In my experience, players get more annoyed when their characters are poisoned then when they lose hit points to regular damage. The latter causes some worry, but the former is more annoying. Suddenly they can't use some of their feats or abilities or spells, and have to apply penalties everywhere, etc.
Now, in a game where wounds actually give you penalties to do actions, the ideology of poisons=bad but weapons=neutral might be different.
Another thought is that D&D is usually set in a pseudomedieval setting, and people in medieval times generally thought poison was evil, so this would carry over into the game ideology. Poison was seen as something that only wicked people use (part of the basis of the Assassin class being evil only, I imagine). So people in the culture don't like it. If evil is culturally defined, this makes poison use evil.
If evil is objectively defined, then something might be evil even if the PC's don't fully understand why. The gods, being wise, do understand why. So the poison use could be evil, but the gods cannot explain to people why, because such matters are beyond mortal comprehension. That could work.
Or maybe there is nothing evil about using poison at all. Just a dirty trick, unfair practice, so not honorable, so no paladins can use it. If you are not defeating your enemy at full power, then how can you "prove" that good always triumphs over evil"? That sort of thing.
If I recall, in 1st ed., only paladins and good clerics were outright prohibited from using poison, but any evidence of using poison could cause a hue and cry for the watch, or subject one to immediate attack (in the description of the 1st ed. assassin class). Mind you, my memory may be faulty here.
I don't think the core rules say that poison use is evil as such, yet. The BoED apparently does, and since that is from the wotc company, and is not tied to a particular setting, I would assume that this idea is going to be carried forward in other wotc products, sage advice, etc. Interesting. I'd say then that Wotc is in the "poison use is objectively evil" camp, and for those who like to apply all the rules as correctly as possible, their window of opportunity to use poison without its being evil is closing.
The talk in BoED of pain and suffering (I haven't read BoED so I am taking others' word for it) seems to translate in game terms as ability loss, which seems to be "worse" than mere hp loss. The ravages are odd, because they cause ability loss, but only to evil creatures (who deserve it, I guess).

But ability loss without pain is not mechanically different from ability loss with pain, so I don't see the issue here. Surely one could develop "painless" poisons that cause ability loss, and not just to evil creatures.
Or maybe not, in D&D. Maybe all poisons, except ravages, cause excrutiating pain, and all sword blows/fireballs, etc. cause absolutely no pain (like the Black Knight in Monty Python). That could explain the difference, and since there is no game effect from losing hp until one gets to 0 hp or less (or one's hp is equal or less than one's subdual damage), this could explain it. I certainly don't recall any PC ever deciding not to do a certain action because they were "in too much pain" when there was no mechanical backup for being in too much pain except low hp. The might say "too wounded" but that is not the same as merely "in too much pain" (see the Black Knight example again).
I mean, one could certainly alter the world to MAKE poison use evil. For instance, have everyone who uses poison, and/or is wounded by poison, become more likely to rise from the grave as undead (that spell that prevents it cannot work on such a being, and there is a 1% chance, cumulative, with every use of poison/having poison used on one). Then there would be an obvious evil side-effect of using or taking poison.
The ultimate verdict? For now, the DM will decide. Check with the DM for what works in that DM's world. If he doesn't like poison use by non-evil characters, then either play under that system or leave. If he does allow poison use, stock up on an antitoxin beer-hat.
For later, I assume no one will be surprised if wotc, the sage, 4th ed., etc., concur in saying that poison use is objectively evil. This would only affect people who play tournament games, or who like to play "by the book", so no big deal for my campaigns.