Perhaps it is a continuity error but in Uncanny X-Men 161 (1982) we were first told of the days when Xavier meet Magneto.
At that time Charles Xavier worked at a clinic for Holocaust victims and had befriended a former concentration camp victim who called himself Magnus. Thus Charles first knew Max Eisenhardt or Erik Lehnsherr simply as Magnus.
Taking a leap of logic [please forgive me here] it might be surmised the writer used that name because to Charles this was a powerful moment and the name harked back to innocent days, days before there was a man called Magneto... when Xavier wouldn't have been able to imagine his friend do something like this.
It was an indictment of the actions Charles Xavier witnessed and a prayer to the past.
Now Mags' name and origins have gone through several alterations over the years, the most notable in recent time was the Magneto Testament (2008) [which was an excellent read]. But at the time of X-Men #25 (1993) the writer might have felt Magnus meant something more to the character and the readers... I for one felt it.