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Doesn't the second sentence mean:
They'll kill him in the same manner they killed his brother.
No, the reader or listener would have to guess that. Instead, say: "They'll kill him the same way they killed his brother." That would make it clear what was meant.
1-They'll kill him, like his brother.
2-They'll kill him like his brother.
The first sentence says that they killed him and that they are going to kill his brother. The second sentence says (possibly) that they will kill him in the same manner that they killed his brother. Neither sentence has a relative clause. In the first sentence, "like" functions as a conjunction. In the second, it functions as an adverb.
If you had a different verb a third meaning would be possible:
They'll take some, like his brother. = his brother took some. It doesn't make much sense with 'kill', though because you can't kill someone twice, however hard you try.
like his brother 
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