Why did no other Houses protest against the Harkonnens? I am sure there must be fugitives from Arrakis to recount what happened in Arrakis.
I am still reading the first book and am reading the chapter which the Count Fenring meets the Baron Harkonnen so no spoilers please. Thanks.
Like @geekosaur says, you need to read on.
There is a very long standing conflict between Houses Atreides and Harkonnen going back many generations. Early in the novel, Leto sends the Baron a letter reinforcing the state of Kanly between them - a formal state of feud/vendetta, in effect war between the houses. The Baron and Pieter discuss that 'the forms have been obeyed' - i.e. the Baron offered to meet to discuss the conflict between them and the Duke rejected this. The conflict between them and the rejected offer of reconciliation underpin the apparent legality of the raid.
The politics in Dune are very complex as you are probably appreciating. Great Houses each rule one or more planets and it would appear that like nation-states, they do conduct war against each other, with various levels of legal and political restraint. The Landstraad appears to be a weak body, largely in-place to allow the Great Houses to band together to counterbalance the power of the Emperor himself.
The Emperor through his edict requiring Leto to take over Arrakis and his disguised Imperial Sardaukar accompanied the Baron's troops - is clearly involved, but in secret for fear of a co-ordinated response from all the Great Houses. Yes, I am sure there would be fugitives - however the size of the attack was so overwhelming, the financial cost to the Baron so high, that these numbers are probably small. Also, with no evidence of Imperial involvement, any report from someone relatively unimportant will either be denounced as fantasy, perhaps even seen as an attempt to make an excuse for Leto's and his troops failure. Also, a minor character would probably be in fear of their life if they emerged to tell stories.
Legal? Unlikely, but the other Houses have no evidence of this involvement even if they suspect. This is realpolitik.
You will need to read on, at least into the second book for some of it, to learn about all of the politics involved. But if you go reread the very beginning, you'll find a mention that Duke Leto is already aware that Arrakis is a trap set for him before they arrive, and that the Padishah Emperor is likely involved (since the grant of Arrakis to House Atreides came from the Emperor); one can guess that the other Houses are equally aware of it, and are wary of becoming involved and thereby possibly becoming a target themselves.
Note that the politics of Dune is quite elaborate, and you may well need multiple rereadings to become aware of all the interacting details.
No, inter-house warfare is perfectly legal, as long as they don't use nuclear weapons. The only illegal part of the invasion is that the emperor interfered. The reason this is bad is because the ruling house is so much more powerful than the rest that it could kill them all off one by one, so if the lesser houses so much as suspect the emperor is attacking any houses they would unite and send the empire into civil war. That is why Shaddam is so secretive about the attack.
And yes there where a few surviving Atreides troops left but most of them were absorbed into the Fremen or smugglers and didn't want to leave Arrakis out of revenge. But even if they wanted to leave they couldn't because the emperor made a deal with the spacing guild so they wouldn't let any Atreides off the planet.
The feud between House Atreides and House Harkonnen go back to the time of the Butlerian Jihad - 10,000 years prior to the events in Dune. This feud is mentioned in the Legends of Dune series. When Frank Herbert died, he left a huge collection of notes on the backstory and motivations of the characters; these were later collected, fleshed out and published by his son Brian. Not everyone likes the posthumously published works, so I'd recommend only reading them after reading all of Frank's books.
Conflicts between "Great Houses" were reasonably common, and as long as the parties did not use "atomics" (nuclear weapons) against each other, they were allowed to proceed as long as they mostly obeyed the ritual terms of "kanly" (which is the name for feuds and/or vendettas).
