Dear Colleague,
I am sorry that I gave you cause to open your mouth and let noises come out—I know how hard it is to find the right words for a grieving coworker.
“I’m so sorry for your loss” can lead to an awkward is-this-a-hug-or-a-double-shoulder-pat. “He’s in a better place” initially seems reassuring. But as experience shows, it rarely comes with a map. “I know exactly what you’re going through” is simply preposterous. It implies that the speaker’s deceased estranged father was also a compulsively hoarding prison psychiatrist. On the other hand, saying “Well, you weren’t that close to him anyway,” may cause the daughter of said compulsively hoarding prison psychiatrist to open her mouth and let noises come out of it. Wookiee noises.  
While there is no best practice for consoling a colleague you barely know, I can assure you that it is incorrect to say to anyone, “Well, you weren’t that close to him anyway.” Your theory that one’s sense of loss is directly proportional to one’s “closeness” to the deceased is really stupid. It is really stupid because it fails to take into consideration the complexities of human relationships. Just as you can grieve for someone you were close to, you can also grieve for the absence of something profound you will never have (e.g., the love of your estranged, compulsively hoarding, prison psychiatrist father).
Needless to say, your comment made me binge on a bitter cocktail of guilt and regret, with the realization that I should have, perhaps, tried harder to build a relationship with my father, especially when he was suffering from both a botched heart valve replacement surgery and tuberculosis. I would have preferred a mimosa.
And while I admit that it may have been especially challenging to procure a single statement that would have both consoled me and alleviated my daddy issues, I wasn’t expecting you to do either of those things—I was merely letting you know why I had missed our meeting.
Naseem Hrab