I never did find a solution, so I ended up deciding to restructure the program.

What I did was set up the main app as a class. Then, I also changed each plugin into a class. Then, as I load plugins using import, I also instantiate the class inside each plugin which has a predefined name, and pass in the reference to the main app class.

This means that each class can directly read and manipulate variables back in the host class simply by using the reference. It is totally flexible because anything that the host class exports is accessible by all the plugins.

This turns out to be more effective and doesn't depend on relative paths and any of that stuff. It also means one Python interpreter could in theory run multiple instances of the host app simultaneously (on different threads for example) and the plugins will still refer back to the correct host instance.

Here's basically what I did:

main.py:

import os, os.path, sys

class MyApp:

    _plugins = []

    def __init__(self):
        self.myVar = 0

    def loadPlugins(self):
            scriptDir = os.path.join ( os.path.dirname(os.path.abspath(__file__)), "plugin" )   
            sys.path.insert(0,scriptDir)
        for plug in os.listdir(scriptDir):
            if (plug[-3:].lower() == ".py"):
                    m = __import__(os.path.basename(plug)[:-3])
                self._plugins.append(m.Plugin(self))

    def runTests(self):
        for p in self._plugins:
            p.test()

if (__name__ == "__main__"):
    app = MyApp()
    app.loadPlugins()
    app.runTests()

plugin/p1.py:

class Plugin:

    def __init__(self, host):
        self.host = host

    def test(self):
        print "from p1: myVar = %d" % self.host.myVar

plugin/p2.py:

class Plugin:

    def __init__(self, host):
        self.host = host

    def test(self):
        print "from p2: variable set"
        self.host.myVar = 1
        print "from p2: myVar = %d" % self.host.myVar

There is some room to improve this, for example, validating each imported .py file to see if it's actually a plugin and so on. But this works as expected.