Yes, the distinction between theory and hypothesis can be important, but a distinction should also be made between popular science and rigorous peer-reviewed literature. Popular science is meant to be easy for the general reader to understand. Often that means using simpler words, as long as they are still accurate in a general way.
In this case, I believe theory is an acceptable word to use. The MW dictionary, for the definition of 'theory', says
2a. "a belief, policy, or procedure proposed or followed as the basis of action"
3a. "a hypothesis assumed for the sake of argument or investigation"
Seems to me that the usage in the article fits either of these definitions well enough.
> The Greek theoria (θεωρία) meant "contemplation, speculation, a looking at, things looked at", from theorein (θεωρεῖν) "to consider, speculate, look at", from theoros (θεωρός) "spectator", from thea (θέα) "a view" + horan (ὁρᾶν) "to see".
"Theory" should refer only to the beatific vision or its analogical precursors in temporal existence achieved through mystical union with the Uncreated Light!
The only reason this Ancient Greek definition holds is because it is a dead language. Prescriptivism cannot stop natural language change. Any "X should only mean Y" statement is a dead-end conservative approach.
> Popular science is meant to be easy for the general reader to understand. Often that means using simpler words
The point above, and I agree, is that the word 'hypothesis' is taught every year in public schools, from elementary school through highschool. Even dropouts should know it, and from what I've seen do know it. At a certain point we've got to stop pandering to morons. Or worse, pandering to what we assume is the level of morons but is actually substantially lower. I don't think the general public is perplexed by that word; anybody who thinks they are is probably underestimating the public. Even if the average Joe on the street isn't disciplined about using the word hypothesis vs theory, they still understand what the word means when they read it.
Even if I know (or can trivially decipher) the definition of a technical word, reading an article saturated with technical words takes more work than reading an article written in more common language. Articles that take more work to read are going to be read by fewer people, and the population of people that do read them is going to be biased to the well-educated.
If you're trying to communicate to the general public something like "Gophers are actually good sometimes", you probably want that message to go beyond the well-educated.
In this case, I believe theory is an acceptable word to use. The MW dictionary, for the definition of 'theory', says
2a. "a belief, policy, or procedure proposed or followed as the basis of action"
3a. "a hypothesis assumed for the sake of argument or investigation"
Seems to me that the usage in the article fits either of these definitions well enough.