I don't think a category is very usual. What is next: a category for adulterers or lieers? It seems to imply an opnion or a judgement and a wiki should just state the fact.
If in the books is described that Jaime (or an other person) commited rape: than add it ot the article. Use the categories for objective criteria that do not imply a judgement.
Not sure if it is possible to include two collapsible elements in one table. It is probably better to use two templates like you suggested or two tables on the same template. Like this.
About showing the change: I think it would be hard to present the changes in the tables in a clear way. What would the Great House row of the table look? "Used to be House Stark, is as of the end of A Storm of Swords" House Bolton.
We should also take into account that it seems that the Manderlys and Stannis do not seem to have accepted this. Although this issue is unrelated to the problem how to show the changes (in nice way)
I think the editor noticed that where Robert really hates Rhaegar, Eddard does not display that emotion. I think this difference is noteworthy. Especially as Robert accused Rhaegar of having raped Eddard's sister. It looks a bit like "the curious incident of the dog in the night-time".
But I agree that "neutral" may be too strong worded. Better to just to state that Eddard's only thought about Rheagar that is mentioned in the books, is that he did not think Rhaegar had frequented brothels.
My preference was to have the info in the templates as of the begin in of the books. And as second option to implement a show/hide for the templates.
I think there was also a suggestion to use a setting to indicate which book should be used as base, the Tower of the Hand has this. But I don't think this is possible with the wiki software.
The Aegon IV article says he was born in 135 as son of Viserys II Targaryen who according his article was born in 122. That makes Viserys 12 (or maybe just 13) when he fathered his child. I guess it is possible but it seems to me a bit implausible
We have been over the spoiler policy a number of times.
I suggested that we should use show / hide tags to prevent spoilers and that death dates should not be included in the family trees. However the majority held the opinion that there would be no prevent spoiler policy so I guess this applies to this as well.