$5 3-table tourney bubble hands - am i doing this right?

blinds are around 250-500, i came to final table with chip lead but got screwed on a hand and am down to like 6k

now we got 6 players (top 5 pay)
i get in a hand and make mid pair on the flop, a guy pushes ontop of my 1k bet for like 3k, i put him on a flush or straight draw and call, he has a flush draw, it hits.

so now i got 66 and move in for 1.5k and get busted.

so my question: should i not play this way at the bubble? I think the call where the guy was on a draw is good, i dont think i should be refusing that edge. is that true?

Then with 66, i probably could have folded my way into the money, but i figured a doubleup would get me back in teh action.

any thoughts? im trying to break into these MTTs playing $5 3 table SNG and $5 MTT, having decent success but doubting myself somewhat