I can see that. I would think they could have used Geller field tech to seal it. Maybe just long enogh for him to I don't know get a sandwich, go to the bathroom, kill Horus. Maybe there are caveats to the tech that prevent it? I don't know much about Geller field fluff so.
While it was said the Chaos gods breached the Emperor's genelab to snatch away the infant primarchs, in the First Heretic we see word bearers getting sent into the past to cut the powerfeed to the geller generators to allow the chaos gods to act. But it remains to be seen if it was actually truth or just a lie planted by chaos. But i suspect it will be retconned to the Sigilite needed to take the Emperor's place on the golden throne to direct the astromonican while he faced Horus as he could not spare any power for it at all. The power need was handled by the unspoken sanction draining mortal psykers to feed it.
The Second Battle of Terra happened shortly after Guiliman's arrival when the Astronomican went out. I feel theres a strong connection between that, and the Emperor actually being awake on the Golden Throne and communing with his son, as he could devote more of his power to it while the beacon is offline. The astronomican didnt come online again until after a high level delegation from mars had arrived to tireless work in the bowels of the golden throne and succeeded after many weeks. When the Astronomican went offline, Khorne immediately lashed Terra with 88 daemonic legions, that wasnt banished until the beacon was restored.