The Raspberry Pi is generally powered from a 5V wall-wart type of DC power supply. The secondary is galvanically isolated from the mains voltage for reasons of personal safety (a fault will not expose the end user to the mains voltage).
The DC return of your bridge rectifier circuit is most certainly not isolated from the mains. The Raspberry Pi ground is 'floating' with respect to the bridge rectifier ground - there is no galvanic connection between them, hence your voltage measurement.
If you were to connect the DC return of the bridge rectifier circuit to the Raspberry Pi ground, you bypass the galvanic isolation that the DC power supply gives you. This means your Raspberry PI is now mains-referenced, and any fault could potentially expose you you to lethal voltages. I wouldn't do this.
A further complication comes if you also hook up an earth-referenced return to the Raspberry Pi, like a connection to a PC, with the mains-reference return connected. When you mix a mains-referenced return like your rectifier circuit with earth, things are going to explode (you essentially short out your bridge through the earthed return, which is often a flimsy wire that gets really hot and melts/catches fire while blowing up everything connected to it). Another reason not to do this.
You would be much better off with a small line frequency transformer to (1) step down the mains voltage to a lower level ahead of your resistive attenuator, and (2) provide galvanic isolation from the mains. Put your bridge and attenuator in the secondary of the transformer. With this, you can safely connect the low voltage isolated rectifier return to the Raspberry Pi return.
(You also must include a fuse in the line to isolate the rectifier circuit from the mains if there is a severe fault like a transformer fault or a short circuit.)
It looks like your output is only going about 4mV below ground. The input offset voltage for the TLC272 is up to 10mV so maybe you need to pick an opamp with a smaller offset. Seeing a schematic would be helpful, too.
Best Answer
A small 1:5 transformer will boost the voltage to the 1.5 to 2.5 V range, which will be enough to light up the LED. A current-limiting series resistor may or may not be needed, but just to be safe, make it 100 Ω to limit the current to 10 mA or so.
The LED can withstand the reverse voltage, so no other rectification should be necessary, but if you're really worried about it, just put an ordinary signal diode in parallel with the LED, pointing the other way.
simulate this circuit – Schematic created using CircuitLab