I agree with you that Seed key is a best way of security if you properly use the seed key then it is the best way of securing your wallet.
The mnemonic seed [1] is not a key. Its purpose is NOT to secure your wallet.
This (random) seed is used to derive all of your private keys.
I am using electrum for more then 2 yrs and my computer got 2 times hacked but they were not able to hack my electrum wallet.
You are definetely doing something wrong.
I assume your pc didn't get 'hacked' but you have downloaded malware.
You should consider using a safer option to store your coins if your pc already has been infected.
The reason the attacker hasn't already stolen your coins probably is that he was kind of incompetent.
Nevertheless, this is in NO WAY related to the mnemonic seed.
[1]
https://en.bitcoin.it/wiki/Mnemonic_phrase