The two references you give (Dt 7:3, Ez 9:12) explicitly help answer your question (though the Ezra one is technically irrelevant since it was centuries after the time of Samson). Both passages list an explicit set of people when a slightly expanded context is shown:
Deut 7:1-3 (KJV)
1When the LORD thy God shall bring thee into the land whither thou
goest to possess it, and hath cast out many nations before thee, the
Hittites, and the Girgashites, and the Amorites, and the Canaanites,
and the Perizzites, and the Hivites, and the Jebusites, seven nations
greater and mightier than thou; 2And when the LORD thy God shall
deliver them before thee; thou shalt smite them, and utterly destroy
them; thou shalt make no covenant with them, nor shew mercy unto them:
3Neither shalt thou make marriages with them; thy daughter thou shalt
not give unto his son, nor his daughter shalt thou take unto thy son.
Ezra 9:1-2, 10-12
1Now when these things were done, the princes came to me, saying, The
people of Israel, and the priests, and the Levites, have not separated
themselves from the people of the lands, doing according to their
abominations, even of the Canaanites, the Hittites, the Perizzites,
the Jebusites, the Ammonites, the Moabites, the Egyptians, and the
Amorites. 2For they have taken of their daughters for themselves, and
for their sons: so that the holy seed have mingled themselves with the
people of those lands: yea, the hand of the princes and rulers hath
been chief in this trespass. ... 10And now, O our God, what shall we say after this? for we have forsaken thy commandments, 11Which thou hast commanded by thy servants the prophets, saying, The land, unto which ye go to possess it, is an unclean land with the filthiness of the people of the lands, with their abominations, which have filled it from one end to another with their uncleanness. 12Now therefore give not your daughters unto their sons, neither take their daughters unto your sons, nor seek their peace or their wealth for ever: that ye may be strong, and eat the good of the land, and leave it for an inheritance to your children for ever.
Note that the Philistines are not listed. This is true even at the time of Israel entering into the Promised Land (during Deuteronomy).1 To my knowledge, the Philistines are never directly stated anywhere in Scripture to be prohibited from marriage to an Israelite.
Additionally, except in the case of a man having only daughters and no sons to pass inheritance to (like Zelophehad's daughters, Num 36), there was not an explicit command that all marriage had to be done between Israelites.
The Philistines likely had conquered and settled or been transplanted to that location,2 and were not part of the people group of Canaan.3 So the Philistines did not originate from the Canaanite groups infected by the Amorite sins (Gen 15:16). The Philistine land was considered separate from the Canaanite land (Ex 13:17), and the people group was distinguished from the Canaanites (Josh 13:1-6).
The Parents' Objection
Undoubtedly the Philistines were the enemies of Israel (Jdg 14:4 mentions their dominion over Israel). They also were a pagan people, worshiping gods other than the God of Israel (Jud 10:6, 16:23). This alone is enough reason as to why the parents objected to Samson's choice. Indeed, any mixed marriage (even with non-forbidden peoples) ran the risk of having the Israelite's heart turn to the pagan gods; and idolatry was expressly forbidden (Dt 11:16). As the verse notes, however, they were not aware how God was working through the request.
So there is no direct conflict with God's commands and His possible moving in the heart of Samson to be attracted to a Philistine woman. However, even if it were sinful of Samson, and arose wholly of him, and God simply allowed it for His own purposes, it could still be something "of the Lord." Whether God is actively doing or passively allowing, He is working. That is simply how God operates in a sinful world. Humans sin, and God works despite that sin.
1 I do not hold to a late date, redacted writing of Deuteronomy, but that it was completely (or nearly so) written by Moses (though parts of last chapter perhaps by Joshua).
2 "1175 BC: Ramses III defeats the Sea Peoples including Philistines and settles captives in fortresses in southern Canaan (alternatively, Philistines invade and settle the coastal plain for themselves)." (http://en.wikipedia.org/wiki/Philistines#History accessed 5-2-2014)
3 "The Philistines, while an integral part of the Canaanite milieu, do not seem to have been ethnic Canaanites, and were listed in the Table of Nations as descendants of Misraim; the Arameans, Moabites, Ammonites, Midianites and Edomites were also considered fellow descendants of Shem or Abraham, and distinct from generic Canaanites/Amorites" (http://en.wikipedia.org/wiki/Canaan#Biblical_usage accessed 5-2-2014)