The problem is that there are two totally different visions of the Prime Directive representing opposing philosophies. The original PD as seen in TOS was a rejection of colonialism, a recognition of the idea that just having superior technology does not make the Federation more qualified to understand another culture's needs than the culture itself, and that if you attempt to impose solutions on a culture from without, you'll inevitably do more harm than good. It's about humility, recognizing the danger of good intentions and the right of other cultures to make their own choices and learn from their own mistakes, rather than fall victim to yours.
But the 24th-century PD seen in "Pen Pals" and "Homeward" is just the opposite. It's lost sight of that humility and turned into "Those primitive cultures are too fragile to understand our knowledge, so we smarter beings are entitled to decide their fate for them even if it destroys them." It's fallen right back into the arrogance of assuming that less advanced societies have no agency, that we have the right to make their choices for them without giving them a say. The only difference is that we're deciding not to intervene under any circumstances rather than deciding to force our ways upon them. But in both cases, it's motivated by the same arrogance, the same belief in our superior right to decide on their behalf.