Thinking in terms of electron current will get you nowhere closer to understanding electronics.
In the end, however, it really doesn't matter. Everything works out even if you reverse conventional current.
In electronics current flows from positive to negative, this is a rule of thumb observed world-wide to keep everyone sane. You can reverse this if you like, it won't change anything in your analysis, but you will confuse everyone you ask for information.
So, to answer your question, it doesn't matter what you consider "out" (source) and what is "in" (sink) in terms of current. A diode still needs a positive voltage across it for current to flow, conventional or otherwise.
It is incorrect to think of electron current as "proper current", because it very much depends on the nature of the device.
For example, in your battery the charge carriers may be anions or cations depending on chemistry. In a transistor the actual charge carriers can be thought of as "virtual" positively charged particles.
What about Transformers and Capacitors? surely current "flows" through these devices, but there are no electrons (or any other charged particle) moving across the gap!
You can, if you like, analyze every component of your circuit in terms of the real charge carriers that produce the current, however this would be an insane thing to do, extremely confusing, error prone, but ultimately provides no benefit to you as a circuit designer
Input vs Output
However, there is a very big difference between a pin that is configured "output" vs one that is configured "input". An "output" pin presents a very low resistance vs an input pin presents a very large resistance.
That is, an output pin can "source" or "sink" current much like a power supply , whereas a pin configured as input has almost no current at all to fulfill its function
Confusingly, using this analysis, both "ground" and "+5V" are output pins, meaning, they both are used to source or sink current and present a very small resistance to anything connected to them.
Colors have no set general meaning, it is very much dependent on context. for example in your house wiring (USA) - Black is hot (Line), White is Neutral and Green is Earth.
Assuming any wire is "ground", red black purple or orange, without verifying is a good way to get hurt.
Ground is just a special name given to the common reference point in a circuit. A complex circuit can have one ground or many grounds, it can even have virtual grounds. Grounds can be isolated or coupled.
Ground has nothing to do with where the electrons come from, its basically just a necessary coincidence that ground is the "source" of electrons with conventional current. All that matters is that is a "fixed point" that you use as a reference.
"Ground" is only meaningful because it is a common reference potential shared across the nodes of a particular circuit, meaning every component has a "leg" on the ground.
This means You could use a -5V power supply, relabel -5V to "Ground" and "0V" to "+5V" Everything will still work exactly as if you used a +5V power supply where "0" is Ground, assuming that the physics of the -5V supply is OK with "reverse" current.