Hector may have pulled the trigger on his best friend (or maybe lover) but Eladio is the one who gave the order. Seems rather weird that Gus wanted Hector to suffer while he gave Eladio a quicker death by poisoning him.
Normally it wouldnt, however Gus was able to win back Eladio’s trust and respect - even to the point where the latter would neglect Hector in favor of Gus. This would lead to Hector also developing a deep hatred back towards Gus in return. Therefore, it was easier for Gus to blame his competition rather than the one whom he works for and is respected in return.