Estrada is 31 years old now and many of those innings from 2011-2015 came as a reliever. He is no longer the pitcher that he was in 2012-13. Projections have him down for an ERA above 4.00 and that includes some relief innings.
Fly ball pitchers give up additional home runs in home run parks, yes. But Estrada limits balls in play to some degree because fly balls have a slightly lower BABIP and he carries a good strikeout rate. For his career, Estrada has given up 26 balls in play per 9 innings. An average pitcher (35% FB%) would let 9.1 of those go for fly balls. Estrada at 45% would allow 11.7 fly balls. The Blue Jays have a ~110 home run factor and Estrada is perhaps slightly homer-prone.
So we'll say with the Blue Jays he's a 12.5% HR/FB guy and with the average team he'd be at 11%. With the Blue Jays, those 2.6 (11.7 - 9.1) extra fly balls will lead to .325 extra home runs per nine, and home runs are worth ~1.7 runs on average, giving us 0.55 extra runs. On the average team, the 2.6 fly balls would give us .286 more home runs, and .49 extra runs.
The penalty is about 0.06 runs per nine. A real difference, but not to the point where you'd explicity decide "we can't have this guy pitch in our ballpark."
Jeff Sullivan wrote a good article about batted balls and ballparks here: http://www.fangraphs.com/blogs/the-significance-of-pitching-to-the-park/