Given how much we understand about stellar mechanics, a sudden, century-long increase in activity is not something that could be ruled out.
The first question is 'are geomagnetic storms that bad?' The answer is, we don't really know. There haven't been many bad ones affecting modern electronics. A big one in 1989 knocked out power in Quebec, but that isn't that big of an area, and the damage was repaired quickly.
The second question is 'could they be worse?' The geomagnetic storms that do hit Earth are like a super-powered solar wind consiting of charge particles. Since they are called a Coronal Mass Ejection, most of the particles discharged are hydrogen atoms (protons, basically) and electrons, with some alpha particles mixed it. The more dangerous parts of a nuclear weapon's EMP are caused by gamma radiation. If a huge gamma burst hit the Earth's atmosphere, it would effectively be worldwide EMP blast, at least on the side facing the sun.
The last question is "is that possible?" Well, solar flares do cause increased gamma emission, but the causes of solar flares are poorly known. So it is hard to say if something external could trigger them. It seems likely that high gamma emission has not happened in the past, because there would probably be evidence of that on Earth.
Far out speculation
One thing that cosmically causes gamma emission is accretion of one object into another, like a star being sucked into a neutron star or black hole. For example, if a Jupiter sized planet appeared out of deep space, approached the sun too closely, and then broke up into a ring, the accretion of the ring material into the sun would cause intense X-ray and/or gamma emission for a (geologically) short period of time; as long as it took the ring material all to settle into the sun.