This is weird right. Marisa turning into a youkai without fulfilling any of the steps a magician needs to do to reject their humanity. Or is zun going to reveal that it is 'forbidden magic' that turns you into a youkai and immortality is just the most common culprit.
It's implied that becoming a Magician the 'proper' way is the safest. It's impossible to become one now in the outside world (or so implied), but within Gensokyo or other 'non-existent' locations it still is. However, even with that, with regards to GSK, Marisa is always running the risk of cascading into becoming some type of sorcery-related youkai. by accident rather than by very, very long term design. This could destabilize the status quo in GSK, and Marisa would likely not be driven by her own will, but by her new nature.
That would make her a target for extermination. While the recurring concept of new ensembles was conceived by Zun more for gameplay reasons, that being each game having a couple of bosses who worked for one big boss, within the lore it also provides for a handful of 'rational' leader youkai, who can help and have a vested interest in maintaining the power balance within GSK rather than wreck it, having absolute power over a couple lesser youkai, so they are also under control. Marisa if she fell within Reimu's lifetime wouldn't easily fall into these categories.
The proper way is something that 1: Marisa is unlikely to actually achieve, at least on her own. Magicians are superlative individuals who can crack the secret of immortality within their lifetimes. Marisa is a resourceful and cunning girl, but she really isn't that type, no matter how much she trains or reads. She isn't a unparallaled genius and she lacks a lot of discipline. And 2. Even if she does do it, it'll be a problem for a later generation of shrine maiden than Reimu, and it's more likely that she'll be a relatively stable presence like Alice anyway.
So Reimu's only real concern is if she turns around now. Which is why Zun keeps re-visting this little plot thread.