The Federation, in the lore I've read, is 'colour-blind' in the sense that it actually doesn't give a damn about your ethnicity from an administrative level. If I remember the Gallente lore dump right, FedGov biographies list 'identification' instead of 'ethnicity' - and sometimes they have neither at all.
To some people, that can be seen as racist. Not having 'positive discrimination' can be rallied against as being racist.
Is there active racism? Not from the administration. Passive? Very possibly, and that increases as you move away from the government and into the people themselves.
There would be the fear of 'they're taking our jobs' in a competitive capitalist society with next to no social safety net. There would be a fear of stability in the 'tried, tested and true' Gallentean way of life when there's a sudden 'flood' of immigrants which, at best are from the Republic and are open to some Federate ideals, but would most likely be straight from the Amarr Empire, freed slaves which, regardless of their views on slavery would still have grown up immersed in Amarrian culture and ideals.
There'd be legitimate 'fear' in the Gallente/Mannar/Caldari/Intaki populations in particular in the Federation about the instability that new Minmatar immigrants may result in. Hell, that fear may also exist in some fully-integrated Minmatar communities.
I don't think that the Federation is racist, it's people on the other hand, I just think they're having typical reactions that a fraction of any human population would have.
Should it be such a big issue in the Federation, I don't know, I really don't.
Is making it about race appropriate for Federation capsuleers, I don't think so. I think it's right for the Federation guys to be like 'um, what even are you talking about, this is just a murder trial' and for Matari capsuleers to be big on 'kin and tribe' and so on (which in itself shows the Gallente traditional way of doing things conflicting with Matari newcomers and their view on things). That's what's been happening, and it'll be interesting to see how it ends up.