"Is fractionation a legitimate aim?"

Of course it is. A majority of Scots may still support the union but that doesn't mean they don't see the SNP's aims as legitimate. And we are talking about the party who are currently the Scottish government here and not some small insignificant fraction of the Scottish electorate. Plus it is an inclusive party (totally unlike the BNP) who's stated stance is that should they achieve independence (among other categories) everyone legally resident in Scotland at that time would be offered citizenship regardless of race, religion, nationality, colour, parentage etc - and to decline citizenship would not be detrimental to their rights of abode etc.