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There is no indication in the text that the Jews were aware that Shimshon was secretly waging a one-man war against the Plishtim. From outward appearances it would seem that a former shofet of the Jews has gone off the derech and married non-Jewish women (though the Rambam indicates that they were converted in hastily convened courts). Furthermore when he died, ostensibly there were no Jews around.
If so why was his body recovered and why was he not viewed as a villain by his contemporary Jews?
I challenge your assumption that no one knew. Consider this episode (Judges 15:9-20):
9 Then the Philistines went up, and pitched in Judah, and spread themselves against Lehi. 10 And the men of Judah said: 'Why are ye come up against us?' And they said: 'To bind Samson are we come up, to do to him as he hath done to us.' 11 Then three thousand men of Judah went down to the cleft of the rock of Etam, and said to Samson: 'Knowest thou not that the Philistines are rulers over us? what then is this that thou hast done unto us?' And he said unto them: 'As they did unto me, so have I done unto them.' 12 And they said unto him: 'We are come down to bind thee, that we may deliver thee into the hand of the Philistines.' And Samson said unto them: 'Swear unto me, that ye will not fall upon me yourselves.' 13 And they spoke unto him, saying: 'No; but we will bind thee fast, and deliver thee into their hand; but surely we will not kill thee.' And they bound him with two new ropes, and brought him up from the rock. 14 When he came unto Lehi, the Philistines shouted as they met him; and the spirit of the LORD came mightily upon him, and the ropes that were upon his arms became as flax that was burnt with fire, and his bands dropped from off his hands. 15 And he found a new jawbone of an ass, and put forth his hand, and took it, and smote a thousand men therewith. 16 And Samson said: With the jawbone of an ass, heaps upon heaps, with the jawbone of an ass have I smitten a thousand men. 17 And it came to pass, when he had made an end of speaking, that he cast away the jawbone out of his hand; and that place was called Ramath-lehi. 18 And he was sore athirst, and called on the LORD, and said: 'Thou hast given this great deliverance by the hand of Thy servant; and now shall I die for thirst, and fall into the hand of the uncircumcised?' 19 But God cleaved the hollow place that is in Lehi, and there came water thereout; and when he had drunk, his spirit came back, and he revived; wherefore the name thereof was called En-hakkore, which is in Lehi unto this day. 20 And he judged Israel in the days of the Philistines twenty years. (Translation from the link above.)
From the beginning of the story we see that the people were not completely oblivious to Shimshon's actions in the Plishti cities. Furthermore, we are only told that Shimshon was a "Judge" here at the end of the story (which I note constitutes one full parshiyah). So the Jews meet him and extradite him, and then the Jews see he survived (and probably hear some stories too) and even accepted him as their Judge! The contrast shows that the Jews realized Shimshon is on their side, so to speak, were willing to accept him as their leader, and very likely realized (to some extent) that he was determined to fight the Plishtim.
As to why his family recovered his body? They heard the story, viewed him as a hero and family member and brought him back for proper burial. I don't really see the question there.
