LEGO's official position on this technique was explained at Brickfest 2006. Jamie Berard, then a relatively new designer in Billund gave an excellent presentation on why certain techniques are considered "illegal" in official sets. The basics message is that building techniques should:
- not stress the bricks
- be suitable for the target audience of the set
He described in some detail the ways that Technic beams and regular system bricks can and cannot be combined in official sets. The main problem areas occur because:
- Technic holes don't exactly line up with the studs on the sides of system bricks
- the holes in Technic beams are slightly smaller than the ones in system bricks
The implications are:
- Although system brick studs can be inserted in the holes in Technic beams, this should be avoided where it would be difficult for children to take apart. Jamie gives an example where a brick has a single stud inserted into a beam, and describes it as "technically legal" (but not recommended). This is the situation in your example.
- Where the combination of Technic and system bricks results in an assembly where components interfere with each other, this can stress the parts. However, this is not the case in the example you cited.
According to these rules, then, the example you give is not illegal. Clearly, it can be a problem under some circumstances, but is acceptable under others.
Unfortunately, none of this actually answers your original question, as there remain two possibilities:
Your assertion that "at one point, LEGO didn't really support putting a stud into a Technic hole, stating that it caused too much stress on the bricks" may not be correct. The misapprehension may have arisen because Lego emphasized the illegal uses of the technique, but down-played legal ones. In that case, we may assume that set designers simply chose not to use the technique (or were unaware that they could because they, too, were misguided).
The alternative explanation is that LEGO did make a sweeping statement to this effect, but later realized that it needed clarification. In which case, Jamie's presentation in 2006 seems to be the first clear public statement of the more detailed rules (of course, internal designers might well have been aware of the policy tweak much earlier, but still chosen not to use the technique). If there was such a policy adjustment, this would establish why the technique was not used until recently.
Without the text of LEGO's earlier communications on the subject, it is difficult to know which explanation is the correct one. Either way, I'd urge you to look at the slides for Jamie's presentation. It is available online in powerpoint format and as a pdf. Apart from being an interesting read in their own right, they also make it clear that this single stud-in-a-hole has been legal since at least 2006.