In theory it could work, but it’s not very intuitive for Mercy to be the only one with jump mapped to her L2. 
I want to keep all “basic” interactions on the same buttons, otherwise it’s probably better to just rethink from the start. And like I mentioned, there’s still the possibility of putting it on two buttons pressed at the same time, or make it somehting she shoots from her gun.
That is the problem with my solution. However, making it be two button presses also wouldn’t be super intuitive because no one else has to push a combination of buttons to make something happen.
Alt fire on her blaster is open, but… this ability is very much a “My buddy is in trouble, I’m gonna debuff his assailant.” reaction thing. That kind of ability maybe doesn’t work when its a weapon swap away… though we could do something insane…?
To OP:
I am not in favor of these changes as a set nor in any one change listed therein
Mercy
Caduceus Staff - healing increased from 50/sec > 55/sec
While in Valkyrie form, Resurrection CD reduced to 5s; Resurrection is auto reset when Valkyrie is used.
Ressurect - Movement speed decreased from -75% > -90%
Cleanse - remove all negative effects from allies within 10m + immune to cc for 3s; 15s CD
You could but whenever Blizzard has changed her it’s always been BAD and everyone is in out rage cause she is supposed to be a main healer but looking at her now she it out healed by off healers on certain maps by Lucio if Lucio isn’t doing the reddit Lucio. This should not happen if Mercy is doing her job right so lets just say i am very nervous about her being changed and do not trust Blizzard to do her right with any changes.
Because she’s balanced? Why change a balanced hero? 
Ah I see. now I understand better where you are coming from.
Comfort bunny?
Mercy 1.0 was balanced with regards to pick-rate, skill skaling, and win-rate. Doesn’t mean the character concept was without issues, like I outlined in my OP.
ROOD!!!
What if, to increase her healing output, when Mercy’s heal beam is on someone a weak you can use a new pulse ability that projects a short ranged aura that slowly heals nearby heroes by like 8-10 HPS? That ways she’s getting value from her team when they’re playing together, not soaking up damage but keeping them alive enough to give the other healer some help while still focusing her tank.
Ok, crazy solution to this is crazy… but its what my brain came up with so… here we go.
Instead of a weapon swap, Mercy’s left click uses her staff, right click uses her blaster. “Switching weapons” shifts her weapons from offense mode to defense mode and back again.
Offense Mode: Damage Boost on LClick, Standard Blaster on RClick
Defense Mode: Heal Beam on LClick, Blaster that only does 5 damage per shot but has a 20% damage done debuff that lasts 1 second.
Then every 10 seconds (12?), Mercy’s next shot is the size of a Symm Orb and has +30% debuff power. So 50% damage reduction on defense blaster, for offense blaster it’d be… -30% move speed?
Reload can still be Inject because Mercy’s blaster auto reloads anyway.
There we go. Both new abilities added with only using 1 extra key that Mercy isn’t using anyway.
I really appreciate all the thought you put into this, but I’m of the philosophy that if it becomes too intricate you need to get back to basics. In this case I think it would mean putting the Damage Reduction on the reload key (and therefor only have it available with the staff out) and remake the Injection into a passive. Others have already been kinda suggesting it, and maybe that would be the way to go. If a passive I’d probably make it like this:
Injection (passive)
Now, this might see a bit unintuitive (why boost when target is critical?) but the idea is that a good Mercy would be able to juggle between the two for maximum efficiency. This would mean that Damage Boost would have to revert so it works when applied instead of when fired (think appying boost on Fire Strike as it hits rather than when it’s cast).