There are many reasons Alec doesn't go ahead and force Isabelle to carry his child the way he did Viola—and what happened to Viola is a large part of that. He would never risk Isabelle's life the way he did Viola's. Between the genetic risk for eclampsia and Isabelle's youth, an easy and safe pregnancy is unlikely. Then there's the problem of how to hide the pregnancy, and what to do with the baby if it's born...like you said, a risk to Alec's image.

However, Alec definitely wants to impregnate Isabelle—a way of deepening their bond, of laying claim to every aspect of her that he can—and plays it looser with contraception than he should. Isabelle has been pregnant by him twice, once at fifteen and once at nineteen or so, the former ending in abortion and the latter ending in miscarriage.