My TL;DR is, No, they shouldn't, but all in all we'll just have to wait and see. What I say here is about all I'm going to say on this thread, I just want to get my thought/voice out there. I'm just going to say, have nothing more to add on my views of the situation, everything's in this reply, and I don't really have the energy to continue on it, apologies for that. I just ask that you respect that, you don't even have to read my full reply I just want it out there so it can float in the endless abyss of the Internet, even if it changes nobody's mind, it's better to get my thought out than to let it sit and boil and bubble till its nothing but vapor.
With Microsoft, Mojang gets a more opportunities, and general ability to do more things with the game and updates that they want to bring out. An example of this being, the security of the accounts. As it was, they'd have to rebuild the accounts from ground up and it could cause issues with some people's accounts, merging with Microsoft has given them the ability to not have to worry about this.
Guessing what the future will hold makes you paranoid of whats to come, we'll see how it goes with the Microsoft account merge; it very much so probably won't do anything people are fearing because its just an account merge, not a full client merge (IE putting Java Edition on Microsoft Store).
But, guess what, we won't know for sure until the time comes.
Microsoft's been pretty kind to the games they've bought, imho at the end of the day we're just going to have to see how it goes. I think for what it's worth, they probably shouldn't, because should best case scenarios happen they get a lot of creative opportunities and tools to make things faster/easier for them to do. Yeah they could do these things without Microsoft, but at the cost of it'd take a lot longer. And last time they took longer than like a month after announcement, people assumed the game was dead and the dev's abandoned it.
There's always going to be a balance of going for money and going for what the community wants. Without money we wouldn't really be able to pay the game because they couldn't maintain their servers, such as login servers, which shuts down skinning as it relies on the accounts to give people their skins, unless you go through texture packs, but that's less fun. It's a necessary evil it's just really whats going to be prioritized more; its a balance. You either have more of one or the other, or a hard to obtain, perfect balance.
Like I said, my honest opinion is that, no, they shouldn't, because even if we're not in "best case scenario," we're not in "worst case scenario" either. They're given more opportunities thanks to the partnership with Microsoft, which generally helps them out. They're not going to get rid of Java and merge it with bedrock; they can't. This would prevent Linux or Mac users from even getting on it, which is a huge portion of money. And Microsoft knows these alternative OS' exist, and the people on them are generally pretty decently stuck to them. Removing Java removes more than it'd give even them. Sure some MIGHT change to Windows because of it, but that's still a huge loss cause not all of them will. Linux will just use Wine or alternative programs they have to get on Bedrock. To add to this, they'd have to give Java users Bedrock for free anyway. If they don't, and they refuse refunds, they lose a really huge chunk of player base. Big no-no. To add to THAT, even if they DID give it free, they can't guarantee many people will actually play it, let alone use the shop. They've cut out HUGE communities because of it.
If they did do this, they'd HAVE to make a compromise that makes the shop less prominent, and continue giving Java users the advantages Java has. (Free Mods, Skins, Etc, created by the community.) A merge would generally just be too difficult between Bedrock and Java, for a risk they probably really aren't willing to take. If they wanted to get rid of Java in the first place, why didn't they? They bought Minecraft/Mojang, they have Bedrock, if they were given as much power as we're scared of them having to even get rid of / merge Java with Bedrock, they would have if that was the plan. They don't need this account merge to do that, at the very least it wouldn't be JUST an account merge, it would've been a full merge with "Merge your account to get bedrock for free." Its pretty clear that this isn't the intent or plan, granted, at least right now. But I still think that they lose more than they gain, between what I mentioned above and also they're competing with Hytale so...they drop Java, Hytale wins easily. Can't lose if there's no competition. Just keeping Java separate and doing as they've been doing is so far working pretty well, it'd be a dumb idea to merge them. To add to this, having java gives them more. They have to split money gain with Mojang. If they get rid of Java thats 1 additional source of income gone, and at best they'll only recover half of those gains. Better to keep Java. If I'm wrong and they do it anyway, then I'm wrong, they did it anyway. I'm human, I can't tell the future. I just think its unfair to suddenly turn pitchforks and bonfire witch hunt when something small happens (my only edit: especially one as predictable as an account merge) when everything's otherwise gone pretty decent.
I won't be replying to replies to this comment, because what I've said is about all I'm going to add to this and care to add, if my point doesn't change your opinion thats fine, everyone is entitled to their own opinion. I don't particularly care about these conversations because I am very much of the mindset of "We'll see what happens."