The check_block_header function (which uses the getblockheader RPC method) is already compatible with pruned blockchains. It's only the getblock RPC that fails on pruned blockchains. The commit you made to change the initialization routine will allow people to use the wrong daemon at startup (e.g. Bitcoin ABC on the regular BTC network) and is dangerous.

For reference, I added support for pruned mode in this commit, with the fork protection and some renaming done here.

You don't need to change the RPC port in both e.g. ~/.litecoin/litecoin.conf and int p2pool/bitcoin/networks/litecoin.py. Changing it in the latter is probably a bad idea, actually. P2pool already checks litecoin.conf for non-default settings, and if any are present (e.g. RPC password or port changes) p2pool will use the litecoin.conf settings instead of the litecoin.py settings. It's only if the user has not changed the default port that p2pool will use the litecoin.py settings. If that's the case, then litecoin.py should point p2pool to the actual default litecoin ports, which are 9333/9332 not 10333/10332. The same applies for Bitcoin Cash.