I made some calculation, though not that excessive, and somewhere lacks the power or proof (aka numbers). My calculations are not based on previous version-new version, but rather "is the CL still worth to have in your city".
On level 8, with an orc city, considering non-premium residences, it seems that a crystal lighthouse could be better than building one more manufactory, though it is not straightforward, and the secondary boost in gain NH should be included, and has to worth at least 5-6 squares! If someone says that the length boost does not affect anything, then a lvl 8 CL is actually worse than an additional manufactory. Please note that the thousand of KP's are NOT calculated in this, the very same way I didn't add anything for the costs of the manufactory, only pop+cult requirements.
The lower the CL's level, the more you have to value those extra 24 minutes of boosts.
If you have premium buildings in your city, your manufactories take less place, and therefor the secondary boost have to have even more value for you. (about 1 more square)
Conclusion: even with the debuff, it could be better than building addition manufactory, but you have to calculate whether it actually worth it.
On the other hand, I can compare my Mountain Hall to the CL. For this comparision I have to tell, that I have bought a lot of premium expansion, and therefor my numbers are only valid from a premium players perspective:
One level of MH increases my production by 221 every 3 hour. Considering a day 4*3 hours and 1*9 hours, thats ~1200-1250 goods per day.
One level of CL increases my "production" aka the chests by 111,5 every chest. Considering a day 3 chests, that's ~330-350 goods per day. (note: I started to overscout 2 months ago, when I started to use the CL for gaining goods, and thus I can only unlock the wizards chapter, but not the halflings, so approximatly 1.5 half chapters ahead of my time)
Seeing this two numbers, I feel like I want to upgrade my MH instead the CL, and I see thousands of KP's that are wasted. And this does not involve the population the MH gives, witch is way better than the NH time-boost, which I can live without.
I couldn't be sure about free players citys, but even if they produce 1/3 of what I produce, and that means about 4-4-3 manufactories, they still should have the MH a few levels ahead of CL, or have to overscout.
A premium player should build the MH to lvl 8 before upgrade the CL to lvl 2, and to lvl 13 before lvl 3.
Conclusion: Non-premium players have now a more balanced version for the two wonders, but for premium players it is no longer balanced, and the KP's involved are flushed down.
Overall conclusion: If you have already built it, you might want to consider not selling it, but you might actually free space up, by selling the CL. If you haven't built it, and you are a non-premium player, you should consider building it, and if you have overscouted by a lot, it is more than likely, you will come better from it. If you are a premium player, do not build this building if you haven't already, because there are other, better things in your disposal.
Edit: I'm not saying that this "feature" is good for me. But that have been said many times...