The やる here can mean "to kill" or "to beat up", depending on context.
See: What does やっちまえ mean?
やられる is its passive form, "to be killed/beaten up".
やられて(い)る here means "to have been killed/beaten up".
This is Possessor's Passive structure (持ち主の受身), a kind of Indirect Passive structure (間接受身構文). E.g.
（私が）泥棒に財布を盗まれた。 ← Possessor's Passive / Indirect Passive
Often translated as: "I had my wallet stolen by a thief."
cf. 泥棒に財布が盗まれた。 ← Direct Passive (直接受身) / Normal Passive
"The/My wallet was stolen by a thief."
(→ Active voice: 「泥棒が財布を盗んだ。」 "A thief stole the/my wallet.")
The 子分 refers to the speaker's men.
So the sentence literally means:
"I had two of my men killed/beaten up by them."
→ "They've killed two of my men." / "They've beaten up two of my men."
(The Direct Passive equivalent would be 「彼らには子分が二人もやられてる。」, and its active voice sentence would be 「彼らは子分を二人もやっている。」 )
For more on Possessor's Passive, you may want to read: