Python program not being started by rc.d in FreeBSD 7.1

This is due to a libc convention for stdio buffering. If stdout is a tty, it is typically line-buffered; fully buffered otherwise.

As others have suggested, passing the -t flag to ssh forces psuedo-tty allocation, and you get line-buffering as a result.

However, you could also explicitly flush stdout to get a similar result, as in:

import sys

print('test1')
sys.stdout.flush()
test1 = sys.stdin.readline() # ctrl+d and .read() effectively closes 
print('test2')               # stdin for the duration
sys.stdout.flush()
test2 = sys.stdin.readline()

print(test1)
print(test2)
# flushing happens implicitly when the stream is closed

Another option, would be to run python in totally unbuffered mode with the -u flag, as in

ssh srvid 'cd; python3 -u test.py'

Additional workarounds can be found in this stackoverflow question.

The program first waited for input. I have entered hell and pressed enter and then ctr+d for eof. Script did not wait for second input, and printed out test1 and test2.

I'm pretty sure the script didn't stop at the second input because you sent it an EOF during the first.

FWIW, I would probably write the python this way, unless you need multi-line input. It's a closer comparison to your bash example, IMO.

#!/usr/bin/env python3

print('test1')
test1 = input() # raw_input() in python 2.x
print('test2')         
test2 = input()

print(test1)
print(test2)

If you run /usr/local/etc/rc.d/apache22 rcvar it will tell you the variable it's looking at, and what it's set to in rc.conf, but if it's starting correctly with start (as opposed to onestart or forcestart) it should start correctly at boot.

If that doesn't give you an immediate answer and solution it's probably easier if you forget about basing your scripts on another one (the Apache script has some extra complexity), and instead start at the beginning with this guide to practical rc.d scripting.
If you follow those instructions you will have to go out of your way to create a non-working script.
As a bonus you'll learn all about how the rc.d sequence works, and be better able to understand and troubleshoot it in the future.