I agree that there are some trees at Disneyland that are irreplaceable. The ficus tree at Alice In Wonderland is a perfect example. The building itself that Alice is in is not much to look at, even with the outdoor track.
That said, it's easy for us to get complacent about trees as the years turn into decades. Often, they grow so huge they dwarf the buildings and obscure the architecture that was Imagineered there in the first place. I think those two sickly trees in front of Pirates are a good example of that. Pirates was originally Imagineered to walk right up to and thus be able to take in the New Orleans architecture easily and allow it to set an Opening Act in your mind as you headed inside. It really is an elegant and beautiful building.
Most 1960's photographs are amateur shots from tourists and don't do the building justice, but this one is pretty good. Notice the bullet ashtray sitting out front by the trashcan! Disneyland used to have those
everywhere.
Then in the late 1980's they redesigned the area to add the bridge in front to help alleviate crowds. They planted those two trees in the queue, a large tree in the planter in front of the queue, and they grew and grew. In 2000 they beefed up the signage in front for Fastpass with a wrought iron archway, pushing the marquee even further out from the bridge, and they planted vines and more shrubbery.
The end result is that by the 2020's you enter the ride through a dark, overgrown tunnel. As you pass under the bridge, the trees then obscure the building from the queue itself, and you can barely tell there's a building there at all!
That bridge will still be there, but it would be nice to be able to see the building again from different angles. Especially when you walk over the bridge above, or are in the queue as you head into the building.
A similar fate met Tomorrowland. They planted a couple of ficus trees at the entrance to the land in 1967, alongside the Bell System show on the left and the Monsanto ride on the right. But the entrance as designed in 1967 was wide open and you could see the clean and sleek buildings framing the land.
Over a half a century later, and those ficus trees grew into monsters (as that type of tree does in the SoCal climate). Now Tomorrowland is a wall of green and it's hard to tell what's back there. The failed New Tomorrowland redesign of 1998 didn't help, but even after the recent rock removals it's still a ficus forest.
There's actually Imagineering behind all of Disneyland's massive trees, and much of that Imagineering is quite good. A little replanting after 50 years would do the park good in several spots. In my opinion.