Will uploading a copy of my paper to Academia.edu harm the journal it’s published in?

Making the paper accessible to everyone who can't look behind the paywall might hurt the journal's publishing company a little bit by diverting some demand. However, it won't really hurt the people you have been dealing with. Moreover, the journal has given you explicit permission to publish a pre-print, so you're not going against their stated request.

At the same time, you are providing a service to

• yourself, by increasing the reach of your paper and the citations that it will receive
• the journal, to the extent that the preprint will attract interest to the journal and to the extent that people will cite the journal version rather than the preprint
• the public who would otherwise not be able to look at the research. This applies in particular to readers outside of academic institutions and to scientists from poor countries.

Please upload your preprint to a freely accessible repository.

Adding a personal experience to @henning's excellent answer.

Many years ago (around 2001) I worked for a company that shall remain nameless, but was responsible for printing the majority of journals worldwide. Although I was only doing reprographics (ie, anything to do with printing / copying that wasn't the journals themselves), just before I left I did some sorting for long term filing (thousands of paper documents being sent off for microfiche scanning).

Being a somewhat boring bit of work, I did end up reading quite a few of them, including a rather interesting email conversation between an editor and the paper's author. Attached were various internal emails where they were trying to find a way around the insistence from the author that they wanted to make a copy available online for free.

End result was basically "the author removed the restriction from the contract before signing, and we can't find any way to force them to change their mind no matter how much we try, so just going to have to left them do it".

While I can't say if there were other similar circumstances with a different outcome, I was going through tens of thousands of pages over the course of several weeks, and visually scanning almost every one, and didn't see any others on that subject. There's obviously also the fact it was around 16 years ago, so things will probably have changed.

While there is a lot of money involved in the journal industry, after basic costs, it's pretty much all profit (that company is sitting on around a third of a billion pounds sterling in the bank, and has well over that in gross profit every year, with well under 50% costs for staff and publishing etc) - but if you want to publish it anywhere else it legally belongs to you, just make sure you only agree and sign to things that you are comfortable doing.

Will uploading it harm the journal or could it generate more interest?

You're overthinking this issue. The people running the journal, who have vastly more relevant information than you do to answer this question, already thought about it, and decided to grant you permission to upload your paper to academia.edu - period. That means there are zero ethical considerations here; you should leave it to those people to think about what's good for the journal instead of second-guessing their decisions, and simply do whatever you think is good for you (and for the rest of society, to the extent that that's something you care about).