Before I respond to this I just want to make clear that I don't think this theory was the writers' intent. I don't think they thought any of this through. But explanations like that are boring, and we're here to discuss, right? Since this seems like the most plausible in-game explanation, I'll attempt to support it.
I think it's mistaken to point to the fact that the Catalyst has been in no danger of being discovered thus far as evidence that opening the relay himself wouldn't introduce the possibility. Why? Because the Catalyst hasn't opened the relay himself yet. It doesn't really tell us much about hypothetical danger. It's equivalent to dismissing the possibility of a stove burning your hand by pointing out that you thus far haven't put your hand on the stove and been burned.
I bolded the above because it does tell us something about what happened to those who did open the relay in the past: the Keepers. We are playing a series in which the last cycle 1) realized the Keepers' role in everything and 2) sabotaged the Keepers' ability to open the relay. What happens when the Catalyst opens the relay himself, and any information gleaned from this event is either 1) utilized by the current cycle, as the Protheans did, and/or 2) passed on to the next cycle to further damage the harvest?
Meanwhile the Catalyst has another option, which is to preserve the illusion that the Reapers are in control of everything. All he needs to do for this is lose one Reaper and two years. Two years is nothing for him, as is one Reaper. It minimized risk while sacrificing essentially nothing.
There are of course questions this brings up. If the Catalyst was so intent to focus attention away from himself, why would be build the dark space relay on the Citadel at all where he lives? If he was so intent on anonymity, why would he risk ME1's events at all? As soon as the signal didn't work he should have just started the Reapers towards the galaxy and not drawn attention to the Citadel. Of course, if we go by Psychevore's theory that no indoctrination exists by the Catalyst onto the Reapers - just the original programming - then it makes more sense that the Catalyst wouldn't be able to flex his plans very well.
You're right, the Star-Child wanting to keep himself a secret is a plausible explanation. I'd actually be willing to go with it, if not for another thought.
Remember, the only reason that the secret about the keepers was discovered by the protheans was because a group of scientists hid in cryo-stasis and then analyzed the situation when they woke up. So let's say that they went to the citadel and sabotaged the keeper and then eventually starved to death (without ever meeting Star-Child because again, Shepard is the first organic to ever encounter him).
What would Star-Child risk by undoing the sabotage when there's no soul around who could detect him?
Also considering that every cycle never fully studied the Citadel, how would anyone know if Star-Child was actually doing anything? How do we know that they wouldn't assume that it was the keepers who did it? After billions of years of practice, I'm certain that Star-Child would be able to nat. 20 on a stealth check with his eyes closed.
Furthermore, considering how absolutely complete that each citadel arrival massacre has been in every cycle, how would information about the Star-Child pass to the next cycle? The Citadel is always wiped clean of evidence of reaper involvement after the reapers complete their cycle of extinction. Even the keeper discovery could only had been made after years of research and only after the reapers were safely gone. It also helped that the scientists had completed a prototype one-way mass relay that directly leads to the Citadel so that they could do something with their discovery.
And if we go with the thought that Star-Child couldn't open the relay himself or undo the sabotage (a giant stretch all things considered) why wouldn't he just order Harbinger and the reapers to start taking the long way to the galaxy ahead of time?
Why didn't the Star-Child have the keepers disable the other half of the Conduit after the scientists used it and starved to death? Why not cut off it's power himself? The Star-Child did design and create the entire mass relay network, would a miniature relay be beyond it's understanding to shut off?
Granted, these are all very nitpicky questions. Though I'd point out that this is a nitpicky detailed genre where details and explanations on how things work matter. So when you have a concept that doesn't make sense where even plausible self-thought explanations only lead to more questions and more questions within those questions, there's a problem.