The article you refer to mentions the Helghast producing and selling "energy" to passing ships (most likely meaning fuel), and other articles/the timeline refer to ships stopping at the station above Helghan for maintenance and refueling, and tankers moving between Helghan and Vekta.
However, the article on Petrusite still clearly states that Petrusite was only discovered in the "early 2350s", just a few years before Killzone 1, as does the article on Arc Technology.
Given your explanation requires that a) we assume canonical information on a fairly major/important subject to be wrong, and b) it opens up all sorts of plotholes and questions about why such a unique and valuable resource wasn't seized and researched by the ISA/UCN (attempted explanation of which would likely raise further questions/plotholes), the much simpler explanation is that whatever fuel the Helghans were selling/transporting in the early days, it wasn't Petrusite.
Given the first article, the take from selling energy was the primary profit, and it prompted the expansion of Helghan space assets into a shipyard (along with readily accessible mineral supply). If all the fuel is coming from Vekta...why not sell at Vekta where you don't burn some shipping it to a whole different planet first? And if you're bringing it to your customers, why not go closer to Earth then Helghan, which is nearly at the end of the journey to/back from Alpha Centauri?
For that matter, at the peak of the Helghan corporations power, before the war crippled them and the exodus and depression ruined their best equipment (if the industrial stuff was lost because it was too expensive, research equipment definitely went first), how could they not discover Petrusite? One of the most prominent and energetic materials on their new gold-mine that they were specifically studying for years?
Finally, as for the ISA...a government made a stupid decision regarding resources? How shocking? /s
First off, Helghan is almost at literally the opposite end of known space from Earth. They might have made a profit supplying Petrusite as an easier/cheaper alternative plasma fuel, but I wouldn't want to heavily invest my planets energy generation on a unique resource extremely far away from me. Second, do you really think the energy situation is all that different from now? If not even worse what with the over population and energy crisis that prompted the exodus. I imagine it's just that instead of Oil and Gas being the big juggernauts, its moved over to Nuclear monopoly. And while the Helghan Corporation made a profit on their own energy...they didn't come anywhere near dominating Earth (going by the whole war and destruction thing), and moved most of their assets of world to Alpha Centauri. I imagine there's still an energy monopoly on Earth, even stronger and more strangling then IRL ones, and it has zero interest in weakening it's position with alternatives outside it's grasp. And since no one knew Petrusite could be weaponized so well yet...the other major motivation for seizing it doesn't exist.
Now compare all that to the canon explanation that just no one discovered Petrusite until the backwards and dictatorial regime that took over the Helghan Administration LONG after their best scientific resources were lost? And all the energy for the costly founding of Vekta and the destroyed Shipyards came from the wealthy and totally unlisted deposits of fissile minerals and/or helium-3 fusion fuel (primarily accepted to be a gas-giant thing, not something you find in large amounts on any physical planet)?
Hell, the modern Helghast's lack of scientific expertise is flat out canon. The real reason they made the first Extra Solar invasion was not to reclaim Vekta (yet), but to steal technical information on the ISA Navy in order to copy it(which they eventually got from the wrecks of the counter-invasion). Before that they literally just had old cargo ships with guns and boarding pods strapped on. They had shitty tech and they knew it. But somehow they also discovered and rapidly advanced the weirdest element in the universe into some of the most complicated and demanding weapons systems in existence (the damn giant anti-orbital lightning cannons)? Something stinks here.
There are plenty of plot-holes, but I'd say the 'canon' one is worse in that regard. If Petrusite is already a known thing, and the Helghast Empire is merely building off the old work of the Helghan Administration? Work it just took them a century to follow up on because the needs of a colony were a greater priority? That makes a lot more sense then everybody missing the single most abundant exotic resource on a heavily industrialized planet for decades.