Did you replace the heads with the exact same brand and style? If you did that, then you could have simply exposed the top of the head, unscred it, removed the 'guts' and spring and replaced it with the new 'guts', spring and top leaving only the old body still in the ground.
Was the replacemant head the same length as the old heads?
If connected to a tee, the nipple could either be too long or not in the fitting or the head deep enough. If you backfilled the soil aroung the heads with out compressing it, the soil around the heads would have compressed over time and given you the impression the the heads were up, when actually, the soil is down.
The biggest reason that I don't install systems with a vertical tee is that there is no 'give' if a hard object comes in contact with the sprinkler head. Either the head, the tee, or the pipe will break. If the lines are installed with the tee flat, or horizontal with a swing joint or a flex joint, then there is a lot more 'give' in the line. This way the head has flexibility in all directions. At the most you might have to replace a marlex fitting, but that is simple and costs pennies. It's also a lot easier to place the head at the exact height of the turf when backfilling.
Give me a few minutes and I'll get some pictures of the two styles.
Mick