The Spear hurts, but it's super iconic to Nidalee and her only real way of exposing her power in a one on one situation. You're not exactly going to put down a Bushwhack mid combat and expect to trigger a Hunt. If you're not CC'd it's not the hardest thing in the world to dodge. Can I do it? No, not very well, but that's my problem more than anyone else's.
Thing is, Nidalee is an assassin, and all assassins are painful when they have the jump on you along with someone that enables their pattern, or if they've positioned or found an opportunity to exploit their pattern to the fullest (like using wall cover to hide the spear's flight to maximize the damage). The Nuclear tipped poke spears of doom are gone, it's just now when you do take a 250 magic damage spear to the back of the head, you're next fear is of outright exploding from an AP, Non-Stealth Rengar instead of simply sighing and having to go back to base.
I would guess that problem with the spears isn't so much the spears, it's that she maintains a poke pattern along with her with assassination and support patterns.
So, to me, she should probably have a primary pattern and a fallback pattern to be healthy, and I'd rather her primary pattern was assassination (as it is in live) and poke was her fallback pattern. Right now, though, poke is just what she winds up doing because she's so good at it, due to probably the cooldown on Spear. Except she's also good at sustaining a siege because of her support-light pattern in her heal, so counterpoke doesn't have as much of an effect.
Things I would do, personally, is increase the general cooldown on Javelin Toss to 9 seconds. With max CDR, she's throwing it once every 5.4 seconds, which achieves roughly what the reverse Varus treatment you've described would do as well. But there's also an opportunity to do a +10/-10 thing here. Nerfed cooldown, sure, but give Swipe a Hunt bonus to reduce it. Swipe Hunt Bonus: Reduces the cooldown of Javelin Toss by 33%. So at level 3, with Q, W, and E in play, she can JT a target, Pounce them and swipe them so that she has a JT ready again if she needs to re-engage like she currently does on live.
I'd also personally get rid of her heal alltogether and give it a Spell Vamp / Lifesteal paradigm, which encourages fighting rather than jumping out and burst healing. Primal Surge: Nidalee evokes the spirit of the cougar, granting an allied champion Lifesteal, Spell Vamp, and bonus attack speed for 5 seconds. If Nidalee uses Primal Surge on herself, her next attack triggers a Hunt. I don't think the Heal is abusive, I Just don't think it fits at all and think it's an opportunity to give her power in other ways. Functionally speaking, if she gets a full Hunt combo off on an enemy with the Spell Vamp and Lifesteal, she'd probably heal for as much or more than her current heal, but at least then she has to spend the time attacking.
I mean, what aspect of a predatory cat heals people? Ain't no one I know isn't allergic to cats. They're the opposite of health.
[[ P.S. Primal Surge granting Spell Vamp / Lifesteal is also a reference to the old summoner spell Surge and the passive on
, so... y'know. I'm basically super clever ]]